| 2568 |
22 Aug 06 |
nicklas |
1 |
<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd"> |
| 2568 |
22 Aug 06 |
nicklas |
2 |
<!-- |
| 2568 |
22 Aug 06 |
nicklas |
3 |
$Id$ |
| 2568 |
22 Aug 06 |
nicklas |
4 |
|
| 5091 |
31 Aug 09 |
nicklas |
Copyright (C) 2006 Jari Häkkinen, Nicklas Nordborg, Martin Svensson |
| 2568 |
22 Aug 06 |
nicklas |
6 |
|
| 2568 |
22 Aug 06 |
nicklas |
7 |
This file is part of BASE - BioArray Software Environment. |
| 2568 |
22 Aug 06 |
nicklas |
8 |
Available at http://base.thep.lu.se/ |
| 2568 |
22 Aug 06 |
nicklas |
9 |
|
| 2568 |
22 Aug 06 |
nicklas |
10 |
BASE is free software; you can redistribute it and/or |
| 2568 |
22 Aug 06 |
nicklas |
11 |
modify it under the terms of the GNU General Public License |
| 4477 |
05 Sep 08 |
jari |
12 |
as published by the Free Software Foundation; either version 3 |
| 2568 |
22 Aug 06 |
nicklas |
13 |
of the License, or (at your option) any later version. |
| 2568 |
22 Aug 06 |
nicklas |
14 |
|
| 2568 |
22 Aug 06 |
nicklas |
15 |
BASE is distributed in the hope that it will be useful, |
| 2568 |
22 Aug 06 |
nicklas |
16 |
but WITHOUT ANY WARRANTY; without even the implied warranty of |
| 2568 |
22 Aug 06 |
nicklas |
17 |
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the |
| 2568 |
22 Aug 06 |
nicklas |
18 |
GNU General Public License for more details. |
| 2568 |
22 Aug 06 |
nicklas |
19 |
|
| 2568 |
22 Aug 06 |
nicklas |
20 |
You should have received a copy of the GNU General Public License |
| 4509 |
11 Sep 08 |
jari |
21 |
along with BASE. If not, see <http://www.gnu.org/licenses/>. |
| 2568 |
22 Aug 06 |
nicklas |
22 |
--> |
| 2568 |
22 Aug 06 |
nicklas |
23 |
<html> |
| 2568 |
22 Aug 06 |
nicklas |
24 |
<head> |
| 2568 |
22 Aug 06 |
nicklas |
25 |
<title>BASE - Test procedures for predefined roles</title> |
| 4633 |
10 Nov 08 |
martin |
26 |
<link rel=stylesheet type="text/css" href="../../historical/styles.css"> |
| 2568 |
22 Aug 06 |
nicklas |
27 |
</head> |
| 2568 |
22 Aug 06 |
nicklas |
28 |
<body> |
| 2568 |
22 Aug 06 |
nicklas |
29 |
|
| 2568 |
22 Aug 06 |
nicklas |
30 |
<div class="navigation"> |
| 2568 |
22 Aug 06 |
nicklas |
31 |
<a href="../../index.html">BASE</a> |
| 2568 |
22 Aug 06 |
nicklas |
32 |
<img src="../../next.gif"> |
| 2583 |
24 Aug 06 |
nicklas |
33 |
<a href="../index.html">Test procedures</a> |
| 2583 |
24 Aug 06 |
nicklas |
34 |
<img src="../../next.gif"> |
| 2583 |
24 Aug 06 |
nicklas |
35 |
Predefined roles |
| 2568 |
22 Aug 06 |
nicklas |
36 |
</div> |
| 2568 |
22 Aug 06 |
nicklas |
37 |
|
| 2568 |
22 Aug 06 |
nicklas |
38 |
<h1>Test procedures for predefined roles</h1> |
| 2568 |
22 Aug 06 |
nicklas |
39 |
|
| 2568 |
22 Aug 06 |
nicklas |
40 |
<div class="abstract"> |
| 2568 |
22 Aug 06 |
nicklas |
41 |
<p> |
| 2568 |
22 Aug 06 |
nicklas |
42 |
This document defines a procedure for testing that |
| 2568 |
22 Aug 06 |
nicklas |
43 |
the predefined roles can perform their work as intended. The main |
| 2568 |
22 Aug 06 |
nicklas |
44 |
purpose is to weed out permission problems resulting from: |
| 2568 |
22 Aug 06 |
nicklas |
45 |
</p> |
| 2568 |
22 Aug 06 |
nicklas |
46 |
|
| 2568 |
22 Aug 06 |
nicklas |
47 |
<ul> |
| 2568 |
22 Aug 06 |
nicklas |
48 |
<li>Incorrect permissions installed by installation program</li> |
| 2568 |
22 Aug 06 |
nicklas |
49 |
<li>Bugs in the permission handling in the core</li> |
| 2568 |
22 Aug 06 |
nicklas |
50 |
<li>Incorrect handling of permissions in the web client</li> |
| 2568 |
22 Aug 06 |
nicklas |
51 |
</ul> |
| 2568 |
22 Aug 06 |
nicklas |
52 |
|
| 2568 |
22 Aug 06 |
nicklas |
53 |
<p> |
| 2568 |
22 Aug 06 |
nicklas |
54 |
The test procedure also tests that the |
| 2568 |
22 Aug 06 |
nicklas |
55 |
basic functionality is working: |
| 2568 |
22 Aug 06 |
nicklas |
56 |
</p> |
| 2568 |
22 Aug 06 |
nicklas |
57 |
|
| 2568 |
22 Aug 06 |
nicklas |
58 |
<ul> |
| 2568 |
22 Aug 06 |
nicklas |
59 |
<li>Creating items and linking them to other items</li> |
| 2568 |
22 Aug 06 |
nicklas |
60 |
<li>Defining import file formats</li> |
| 2568 |
22 Aug 06 |
nicklas |
61 |
<li>Importing array LIMS data</li> |
| 2568 |
22 Aug 06 |
nicklas |
62 |
<li>Importing and validating raw data against array LIMS data</li> |
| 2682 |
02 Oct 06 |
jari |
63 |
<li>Running analysis plug-ins</li> |
| 3873 |
23 Oct 07 |
nicklas |
64 |
<li>Using files instead of the database for storing data</li> |
| 2568 |
22 Aug 06 |
nicklas |
65 |
</ul> |
| 2568 |
22 Aug 06 |
nicklas |
66 |
|
| 2568 |
22 Aug 06 |
nicklas |
67 |
<b>Contents</b><br> |
| 2568 |
22 Aug 06 |
nicklas |
68 |
<ol> |
| 2568 |
22 Aug 06 |
nicklas |
69 |
<li><a href="#summary">Summary of the test procedure</a></li> |
| 2568 |
22 Aug 06 |
nicklas |
70 |
<li><a href="#root">Root user tests</a></li> |
| 2682 |
02 Oct 06 |
jari |
71 |
<li><a href="#admin">Administrator tests</a></li> |
| 2568 |
22 Aug 06 |
nicklas |
72 |
<li><a href="#power">Power user tests</a></li> |
| 2568 |
22 Aug 06 |
nicklas |
73 |
<li><a href="#user">User tests</a></li> |
| 2568 |
22 Aug 06 |
nicklas |
74 |
<li><a href="#analysis">Analysis tests</a></li> |
| 2568 |
22 Aug 06 |
nicklas |
75 |
</ol> |
| 2568 |
22 Aug 06 |
nicklas |
76 |
|
| 2568 |
22 Aug 06 |
nicklas |
77 |
<p class="authors"> |
| 2568 |
22 Aug 06 |
nicklas |
78 |
<b>Last updated:</b> $Date$ |
| 2568 |
22 Aug 06 |
nicklas |
79 |
</p> |
| 2568 |
22 Aug 06 |
nicklas |
80 |
</div> |
| 2568 |
22 Aug 06 |
nicklas |
81 |
|
| 2568 |
22 Aug 06 |
nicklas |
82 |
|
| 2568 |
22 Aug 06 |
nicklas |
83 |
<a name="summary"></a> |
| 2568 |
22 Aug 06 |
nicklas |
84 |
<h2>1. Summary of the test procedure</h2> |
| 2568 |
22 Aug 06 |
nicklas |
85 |
|
| 2568 |
22 Aug 06 |
nicklas |
86 |
<p> |
| 2568 |
22 Aug 06 |
nicklas |
87 |
Here is a summary of the test procedure: |
| 2568 |
22 Aug 06 |
nicklas |
88 |
</p> |
| 2568 |
22 Aug 06 |
nicklas |
89 |
|
| 2568 |
22 Aug 06 |
nicklas |
90 |
<ol> |
| 2568 |
22 Aug 06 |
nicklas |
91 |
<li>Always start with a fresh installation.</li> |
| 2568 |
22 Aug 06 |
nicklas |
92 |
|
| 2568 |
22 Aug 06 |
nicklas |
93 |
<li>The root user creates an administrator.</li> |
| 2568 |
22 Aug 06 |
nicklas |
94 |
|
| 3873 |
23 Oct 07 |
nicklas |
95 |
<li>The administrator creates more users and some global resources: |
| 3873 |
23 Oct 07 |
nicklas |
96 |
<ul> |
| 3873 |
23 Oct 07 |
nicklas |
97 |
<li>A group and three other users. One power user, one user and one guest.</li> |
| 3873 |
23 Oct 07 |
nicklas |
98 |
<li>File formats for importing reporters</li> |
| 3873 |
23 Oct 07 |
nicklas |
99 |
<li>Imports reporters</li> |
| 3873 |
23 Oct 07 |
nicklas |
100 |
</ul> |
| 3873 |
23 Oct 07 |
nicklas |
101 |
</li> |
| 2568 |
22 Aug 06 |
nicklas |
102 |
|
| 2568 |
22 Aug 06 |
nicklas |
103 |
<li>The power user creates item related to the project management: |
| 2568 |
22 Aug 06 |
nicklas |
104 |
<ul> |
| 2568 |
22 Aug 06 |
nicklas |
105 |
<li>A project</li> |
| 2568 |
22 Aug 06 |
nicklas |
106 |
<li>Protocols, one for each type of action: sampling, extraction, etc.</li> |
| 2568 |
22 Aug 06 |
nicklas |
107 |
<li>Hardware and software that are used in the project</li> |
| 2568 |
22 Aug 06 |
nicklas |
108 |
<li>Annotation types for annotations used in the project</li> |
| 3873 |
23 Oct 07 |
nicklas |
109 |
<li>File formats for importing plates, print maps and raw data</li> |
| 5260 |
04 Mar 10 |
nicklas |
110 |
<li>Array LIMS information - plate type, plates, array design, array batch and array slides</li> |
| 5260 |
04 Mar 10 |
nicklas |
111 |
<li>Biomaterial LIMS information - bioplate type</li> |
| 2568 |
22 Aug 06 |
nicklas |
112 |
</ul> |
| 2568 |
22 Aug 06 |
nicklas |
113 |
</li> |
| 2568 |
22 Aug 06 |
nicklas |
114 |
|
| 2568 |
22 Aug 06 |
nicklas |
115 |
<li>The user creates items related to an actual experiment: |
| 2568 |
22 Aug 06 |
nicklas |
116 |
<ul> |
| 5260 |
04 Mar 10 |
nicklas |
117 |
<li>Biomaterials: bioplate, biosources, samples, extracts, etc.</li> |
| 5788 |
06 Oct 11 |
nicklas |
118 |
<li>Experiment: physical bioassays, derived bioassays, raw bioassays</li> |
| 2568 |
22 Aug 06 |
nicklas |
119 |
<li>Import raw data</li> |
| 2568 |
22 Aug 06 |
nicklas |
120 |
</ul> |
| 2568 |
22 Aug 06 |
nicklas |
121 |
</li> |
| 2568 |
22 Aug 06 |
nicklas |
122 |
|
| 2568 |
22 Aug 06 |
nicklas |
123 |
<li>Both the user and the guest then do some analysis: |
| 2568 |
22 Aug 06 |
nicklas |
124 |
<ul> |
| 2568 |
22 Aug 06 |
nicklas |
125 |
<li>Create a root bioassay set</li> |
| 2568 |
22 Aug 06 |
nicklas |
126 |
<li>Filter the bioassay set</li> |
| 2682 |
02 Oct 06 |
jari |
127 |
<li>Run a normalization plug-in</li> |
| 2568 |
22 Aug 06 |
nicklas |
128 |
<li>Check the result by listing and plotting the data</li> |
| 2568 |
22 Aug 06 |
nicklas |
129 |
</ul> |
| 2568 |
22 Aug 06 |
nicklas |
130 |
</li> |
| 2568 |
22 Aug 06 |
nicklas |
131 |
</ol> |
| 2568 |
22 Aug 06 |
nicklas |
132 |
|
| 2568 |
22 Aug 06 |
nicklas |
133 |
<p> |
| 2568 |
22 Aug 06 |
nicklas |
134 |
These tests can also be run in automated mode by test programs. This will of |
| 2568 |
22 Aug 06 |
nicklas |
135 |
course not test the web client, but are useful if one quickly needs to do |
| 2568 |
22 Aug 06 |
nicklas |
136 |
parts of the test and then continue with, for example, the user or analysis tests |
| 2568 |
22 Aug 06 |
nicklas |
137 |
on the web. |
| 2568 |
22 Aug 06 |
nicklas |
138 |
</p> |
| 2568 |
22 Aug 06 |
nicklas |
139 |
|
| 2568 |
22 Aug 06 |
nicklas |
140 |
<p> |
| 2568 |
22 Aug 06 |
nicklas |
141 |
The data files needed by the tests are NOT included in the subversion repository. |
| 2568 |
22 Aug 06 |
nicklas |
142 |
The main reason is that they are too large, and that we don't have permission to |
| 2583 |
24 Aug 06 |
nicklas |
143 |
make them publicly available for download. To get the test file you need to be a |
| 2583 |
24 Aug 06 |
nicklas |
144 |
core developer. Read the instructions on the |
| 7982 |
14 Jun 21 |
nicklas |
145 |
<a href="https://base.thep.lu.se/wiki/DeveloperInformation">DeveloperInformation</a> |
| 5788 |
06 Oct 11 |
nicklas |
146 |
page, <code>Test data</code> section on the BASE web site. The automated |
| 3873 |
23 Oct 07 |
nicklas |
147 |
test programs require that file are placed (checked out) in the 'testdata' |
| 3873 |
23 Oct 07 |
nicklas |
148 |
directory located in the BASE root directory. NOTE! Some test data files are |
| 5788 |
06 Oct 11 |
nicklas |
149 |
bzip-compressed. Use the automatic unpacking that is built-in to BASE when |
| 5788 |
06 Oct 11 |
nicklas |
150 |
uploading. |
| 2568 |
22 Aug 06 |
nicklas |
151 |
</p> |
| 2568 |
22 Aug 06 |
nicklas |
152 |
|
| 2568 |
22 Aug 06 |
nicklas |
153 |
<p> |
| 3873 |
23 Oct 07 |
nicklas |
154 |
To run the tests do the following: |
| 2568 |
22 Aug 06 |
nicklas |
155 |
</p> |
| 2568 |
22 Aug 06 |
nicklas |
156 |
<ol> |
| 2583 |
24 Aug 06 |
nicklas |
157 |
|
| 2568 |
22 Aug 06 |
nicklas |
158 |
<li>Compile the core and the test programs: <code>ant main test</code>.</li> |
| 2568 |
22 Aug 06 |
nicklas |
159 |
|
| 2568 |
22 Aug 06 |
nicklas |
160 |
<li>Change to the <code>build/test/</code> directory.</li> |
| 2568 |
22 Aug 06 |
nicklas |
161 |
|
| 4633 |
10 Nov 08 |
martin |
162 |
<li>Run test programs: <code>./test.sh roles [OPTION] <cmds></code> where |
| 2568 |
22 Aug 06 |
nicklas |
163 |
<code><cmds></code> is one or more of the following: |
| 2568 |
22 Aug 06 |
nicklas |
164 |
<ul> |
| 2568 |
22 Aug 06 |
nicklas |
165 |
<li><code>all</code>: run all tests</li> |
| 2568 |
22 Aug 06 |
nicklas |
166 |
<li><code>root</code>: run the root user tests</li> |
| 2568 |
22 Aug 06 |
nicklas |
167 |
<li><code>admin</code>: run the administrator tests</li> |
| 2568 |
22 Aug 06 |
nicklas |
168 |
<li><code>power</code>: run the power user tests</li> |
| 2568 |
22 Aug 06 |
nicklas |
169 |
<li><code>user</code>: run the regular user tests</li> |
| 2568 |
22 Aug 06 |
nicklas |
170 |
<li><code>guest</code>: run the guest user tests</li> |
| 2568 |
22 Aug 06 |
nicklas |
171 |
</ul> |
| 4633 |
10 Nov 08 |
martin |
172 |
and <code>OPTION</code> can be none or more of: |
| 4633 |
10 Nov 08 |
martin |
173 |
<ul> |
| 4633 |
10 Nov 08 |
martin |
174 |
<li><code>-b</code>: if the batch importers should be tested</li> |
| 4633 |
10 Nov 08 |
martin |
175 |
</ul> |
| 2568 |
22 Aug 06 |
nicklas |
176 |
</li> |
| 2568 |
22 Aug 06 |
nicklas |
177 |
|
| 2568 |
22 Aug 06 |
nicklas |
178 |
</ol> |
| 2568 |
22 Aug 06 |
nicklas |
179 |
|
| 2568 |
22 Aug 06 |
nicklas |
180 |
<a name="root"></a> |
| 2568 |
22 Aug 06 |
nicklas |
181 |
<h2>2. Root user tests</h2> |
| 2568 |
22 Aug 06 |
nicklas |
182 |
<p> |
| 2568 |
22 Aug 06 |
nicklas |
183 |
The root user creates an administrator which is a server-wide admin. |
| 2568 |
22 Aug 06 |
nicklas |
184 |
</p> |
| 2568 |
22 Aug 06 |
nicklas |
185 |
|
| 2568 |
22 Aug 06 |
nicklas |
186 |
<ol> |
| 2568 |
22 Aug 06 |
nicklas |
187 |
<li> |
| 2568 |
22 Aug 06 |
nicklas |
188 |
Create a new user and set the following |
| 2568 |
22 Aug 06 |
nicklas |
189 |
properties. All other properties may remain unchanged. |
| 2568 |
22 Aug 06 |
nicklas |
190 |
|
| 2568 |
22 Aug 06 |
nicklas |
191 |
<table class="listing" cellspacing="0" cellpadding="2" border="0"> |
| 2568 |
22 Aug 06 |
nicklas |
192 |
<tr> |
| 2568 |
22 Aug 06 |
nicklas |
193 |
<th>Name</th> |
| 2568 |
22 Aug 06 |
nicklas |
194 |
<th>Login/Password</th> |
| 2568 |
22 Aug 06 |
nicklas |
195 |
<th>Quota</th> |
| 2568 |
22 Aug 06 |
nicklas |
196 |
<th>Quota group</th> |
| 2568 |
22 Aug 06 |
nicklas |
197 |
<th>Membership</th> |
| 2568 |
22 Aug 06 |
nicklas |
198 |
</tr> |
| 2568 |
22 Aug 06 |
nicklas |
199 |
<tr> |
| 2568 |
22 Aug 06 |
nicklas |
200 |
<td>Admin</td> |
| 2568 |
22 Aug 06 |
nicklas |
201 |
<td>admin/admin</td> |
| 2568 |
22 Aug 06 |
nicklas |
202 |
<td>Unlimited</td> |
| 2568 |
22 Aug 06 |
nicklas |
203 |
<td>-</td> |
| 2568 |
22 Aug 06 |
nicklas |
204 |
<td>Roles: Administrator</td> |
| 2568 |
22 Aug 06 |
nicklas |
205 |
</tr> |
| 2568 |
22 Aug 06 |
nicklas |
206 |
</table> |
| 2568 |
22 Aug 06 |
nicklas |
207 |
</li> |
| 2568 |
22 Aug 06 |
nicklas |
208 |
</ol> |
| 2568 |
22 Aug 06 |
nicklas |
209 |
|
| 2568 |
22 Aug 06 |
nicklas |
210 |
<a name="admin"></a> |
| 2568 |
22 Aug 06 |
nicklas |
211 |
<h2>3. Administrator tests</h2> |
| 2568 |
22 Aug 06 |
nicklas |
212 |
<p> |
| 2568 |
22 Aug 06 |
nicklas |
213 |
The administrator creates users for a project and gives them permissions |
| 2568 |
22 Aug 06 |
nicklas |
214 |
that are suitable for their role in the project. The administrator also |
| 2568 |
22 Aug 06 |
nicklas |
215 |
sets up quota and group membership. |
| 2568 |
22 Aug 06 |
nicklas |
216 |
</p> |
| 2568 |
22 Aug 06 |
nicklas |
217 |
|
| 2568 |
22 Aug 06 |
nicklas |
218 |
<ol> |
| 2568 |
22 Aug 06 |
nicklas |
219 |
<li> |
| 2568 |
22 Aug 06 |
nicklas |
220 |
Create a new group and set the following properties: |
| 2568 |
22 Aug 06 |
nicklas |
221 |
|
| 2568 |
22 Aug 06 |
nicklas |
222 |
<table class="listing" cellspacing="0" cellpadding="2" border="0"> |
| 2568 |
22 Aug 06 |
nicklas |
223 |
<tr> |
| 2568 |
22 Aug 06 |
nicklas |
224 |
<th>Name</th> |
| 2568 |
22 Aug 06 |
nicklas |
225 |
<th>Quota</th> |
| 2568 |
22 Aug 06 |
nicklas |
226 |
</tr> |
| 2568 |
22 Aug 06 |
nicklas |
227 |
<tr> |
| 2568 |
22 Aug 06 |
nicklas |
228 |
<td>Group A</td> |
| 2568 |
22 Aug 06 |
nicklas |
229 |
<td>1GB</td> |
| 2568 |
22 Aug 06 |
nicklas |
230 |
</tr> |
| 2568 |
22 Aug 06 |
nicklas |
231 |
</table> |
| 2568 |
22 Aug 06 |
nicklas |
232 |
<p> |
| 2568 |
22 Aug 06 |
nicklas |
233 |
</li> |
| 2568 |
22 Aug 06 |
nicklas |
234 |
|
| 2568 |
22 Aug 06 |
nicklas |
235 |
<li> |
| 2568 |
22 Aug 06 |
nicklas |
236 |
Create the following users: |
| 2568 |
22 Aug 06 |
nicklas |
237 |
|
| 2568 |
22 Aug 06 |
nicklas |
238 |
<table class="listing" cellspacing="0" cellpadding="2" border="0"> |
| 2568 |
22 Aug 06 |
nicklas |
239 |
<tr> |
| 2568 |
22 Aug 06 |
nicklas |
240 |
<th>Name</th> |
| 2568 |
22 Aug 06 |
nicklas |
241 |
<th>Login/Password</th> |
| 2568 |
22 Aug 06 |
nicklas |
242 |
<th>Quota</th> |
| 2568 |
22 Aug 06 |
nicklas |
243 |
<th>Quota group</th> |
| 2568 |
22 Aug 06 |
nicklas |
244 |
<th>Membership</th> |
| 2568 |
22 Aug 06 |
nicklas |
245 |
<th>Other</th> |
| 2568 |
22 Aug 06 |
nicklas |
246 |
</tr> |
| 2568 |
22 Aug 06 |
nicklas |
247 |
<tr> |
| 2568 |
22 Aug 06 |
nicklas |
248 |
<td>Power user</td> |
| 2568 |
22 Aug 06 |
nicklas |
249 |
<td>power/power</td> |
| 2568 |
22 Aug 06 |
nicklas |
250 |
<td>1GB</td> |
| 2568 |
22 Aug 06 |
nicklas |
251 |
<td>Group A</td> |
| 2568 |
22 Aug 06 |
nicklas |
252 |
<td>Roles: Power user</td> |
| 2568 |
22 Aug 06 |
nicklas |
253 |
<td>-</td> |
| 2568 |
22 Aug 06 |
nicklas |
254 |
</tr> |
| 2568 |
22 Aug 06 |
nicklas |
255 |
<tr> |
| 2568 |
22 Aug 06 |
nicklas |
256 |
<td>User</td> |
| 2568 |
22 Aug 06 |
nicklas |
257 |
<td>user/user</td> |
| 2568 |
22 Aug 06 |
nicklas |
258 |
<td>1GB</td> |
| 2568 |
22 Aug 06 |
nicklas |
259 |
<td>Group A</td> |
| 2568 |
22 Aug 06 |
nicklas |
260 |
<td>Roles: User</td> |
| 2568 |
22 Aug 06 |
nicklas |
261 |
<td>-</td> |
| 2568 |
22 Aug 06 |
nicklas |
262 |
</tr> |
| 2568 |
22 Aug 06 |
nicklas |
263 |
<tr> |
| 2568 |
22 Aug 06 |
nicklas |
264 |
<td>Guest</td> |
| 2568 |
22 Aug 06 |
nicklas |
265 |
<td>guest/guest</td> |
| 2568 |
22 Aug 06 |
nicklas |
266 |
<td>10MB</td> |
| 2568 |
22 Aug 06 |
nicklas |
267 |
<td>Group A</td> |
| 2568 |
22 Aug 06 |
nicklas |
268 |
<td>Roles: Guest</td> |
| 2568 |
22 Aug 06 |
nicklas |
269 |
<td><i>Multi-user account</i> checked</td> |
| 2568 |
22 Aug 06 |
nicklas |
270 |
</tr> |
| 2568 |
22 Aug 06 |
nicklas |
271 |
</table> |
| 2935 |
17 Nov 06 |
nicklas |
272 |
<p> |
| 2568 |
22 Aug 06 |
nicklas |
273 |
</li> |
| 2935 |
17 Nov 06 |
nicklas |
274 |
|
| 2935 |
17 Nov 06 |
nicklas |
275 |
<li>Give USE permission for the listed users to the following plugins: |
| 2935 |
17 Nov 06 |
nicklas |
276 |
|
| 2935 |
17 Nov 06 |
nicklas |
277 |
<table class="listing" cellspacing="0" cellpadding="2" border="0"> |
| 2935 |
17 Nov 06 |
nicklas |
278 |
<tr> |
| 2935 |
17 Nov 06 |
nicklas |
279 |
<th>User</th> |
| 2935 |
17 Nov 06 |
nicklas |
280 |
<th>Plugins</th> |
| 2935 |
17 Nov 06 |
nicklas |
281 |
</tr> |
| 2935 |
17 Nov 06 |
nicklas |
282 |
<tr> |
| 2935 |
17 Nov 06 |
nicklas |
283 |
<td>Power user</td> |
| 2935 |
17 Nov 06 |
nicklas |
284 |
<td> |
| 2935 |
17 Nov 06 |
nicklas |
285 |
<ul> |
| 2935 |
17 Nov 06 |
nicklas |
286 |
<li>Plate importer</li> |
| 2935 |
17 Nov 06 |
nicklas |
287 |
<li>Reporter map importer</li> |
| 2935 |
17 Nov 06 |
nicklas |
288 |
<li>Print map importer</li> |
| 5788 |
06 Oct 11 |
nicklas |
289 |
<li>GTF reporter map importer</li> |
| 4789 |
24 Feb 09 |
nicklas |
290 |
<li>Array design importer</li> |
| 4789 |
24 Feb 09 |
nicklas |
291 |
<li>Array batch importer</li> |
| 4789 |
24 Feb 09 |
nicklas |
292 |
<li>Array slide importer</li> |
| 2935 |
17 Nov 06 |
nicklas |
293 |
</ul> |
| 2935 |
17 Nov 06 |
nicklas |
294 |
</td> |
| 2935 |
17 Nov 06 |
nicklas |
295 |
</tr> |
| 2935 |
17 Nov 06 |
nicklas |
296 |
</table> |
| 3873 |
23 Oct 07 |
nicklas |
297 |
<p> |
| 2935 |
17 Nov 06 |
nicklas |
298 |
</li> |
| 2935 |
17 Nov 06 |
nicklas |
299 |
|
| 3873 |
23 Oct 07 |
nicklas |
300 |
<li> |
| 3873 |
23 Oct 07 |
nicklas |
301 |
Create file formats (<i>i.e.</i>, plug-in configurations) for importing |
| 3873 |
23 Oct 07 |
nicklas |
302 |
reporters. The formats marked as |
| 3873 |
23 Oct 07 |
nicklas |
303 |
optional are not used in the test procedure, but may be useful to weed |
| 3873 |
23 Oct 07 |
nicklas |
304 |
out import problems, since they allow importing all info from the raw |
| 3873 |
23 Oct 07 |
nicklas |
305 |
data files. You may either enter the regular expressions as specified or |
| 3873 |
23 Oct 07 |
nicklas |
306 |
use the "Test with file" feature. |
| 3873 |
23 Oct 07 |
nicklas |
307 |
|
| 3873 |
23 Oct 07 |
nicklas |
308 |
<table class="listing" cellspacing="0" cellpadding="2" border="0"> |
| 3873 |
23 Oct 07 |
nicklas |
309 |
<tr> |
| 3873 |
23 Oct 07 |
nicklas |
310 |
<th>Name</th> |
| 3873 |
23 Oct 07 |
nicklas |
311 |
<th>Plugin</th> |
| 3873 |
23 Oct 07 |
nicklas |
312 |
<th>Configuration values</th> |
| 3873 |
23 Oct 07 |
nicklas |
313 |
</tr> |
| 3873 |
23 Oct 07 |
nicklas |
314 |
<tr class="oddrow"> |
| 3873 |
23 Oct 07 |
nicklas |
315 |
<td>Reporters for project A</td> |
| 3873 |
23 Oct 07 |
nicklas |
316 |
<td>Reporter importer</td> |
| 3873 |
23 Oct 07 |
nicklas |
317 |
<td> |
| 3873 |
23 Oct 07 |
nicklas |
318 |
<table border="0" cellspacing="0" cellpadding="2"> |
| 3873 |
23 Oct 07 |
nicklas |
319 |
<tr> |
| 5788 |
06 Oct 11 |
nicklas |
320 |
<td><b>File</b></td> |
| 5788 |
06 Oct 11 |
nicklas |
321 |
<td><code>mouse/<br>plates_and_reporters.mouse.v4.37k.txt</code></td> |
| 5788 |
06 Oct 11 |
nicklas |
322 |
</tr> |
| 5788 |
06 Oct 11 |
nicklas |
323 |
<tr> |
| 3873 |
23 Oct 07 |
nicklas |
324 |
<td><i>Data header</i></td> |
| 3873 |
23 Oct 07 |
nicklas |
325 |
<td>384_number\t384_column\t384_row\t384_position\toligo_id.*</td> |
| 3873 |
23 Oct 07 |
nicklas |
326 |
</tr> |
| 3873 |
23 Oct 07 |
nicklas |
327 |
<tr> |
| 3873 |
23 Oct 07 |
nicklas |
328 |
<td><i>Data splitter</i></td> |
| 3873 |
23 Oct 07 |
nicklas |
329 |
<td>\t</td> |
| 3873 |
23 Oct 07 |
nicklas |
330 |
</tr> |
| 3873 |
23 Oct 07 |
nicklas |
331 |
<tr> |
| 3873 |
23 Oct 07 |
nicklas |
332 |
<td><i>Min data columns</i></td> |
| 3873 |
23 Oct 07 |
nicklas |
333 |
<td>5</td> |
| 3873 |
23 Oct 07 |
nicklas |
334 |
</tr> |
| 3873 |
23 Oct 07 |
nicklas |
335 |
<tr> |
| 3873 |
23 Oct 07 |
nicklas |
336 |
<td><i>Name</i></td> |
| 3873 |
23 Oct 07 |
nicklas |
337 |
<td>\oligo_id\</td> |
| 3873 |
23 Oct 07 |
nicklas |
338 |
</tr> |
| 3873 |
23 Oct 07 |
nicklas |
339 |
<tr> |
| 4626 |
05 Nov 08 |
nicklas |
340 |
<td><i>External ID</i></td> |
| 3873 |
23 Oct 07 |
nicklas |
341 |
<td>\oligo_id\</td> |
| 3873 |
23 Oct 07 |
nicklas |
342 |
</tr> |
| 3873 |
23 Oct 07 |
nicklas |
343 |
<tr> |
| 3873 |
23 Oct 07 |
nicklas |
344 |
<td><i>Description</i></td> |
| 3873 |
23 Oct 07 |
nicklas |
345 |
<td>\description_Ensembl*\</td> |
| 3873 |
23 Oct 07 |
nicklas |
346 |
</tr> |
| 3873 |
23 Oct 07 |
nicklas |
347 |
<tr> |
| 3873 |
23 Oct 07 |
nicklas |
348 |
<td><i>Gene symbol</i></td> |
| 3873 |
23 Oct 07 |
nicklas |
349 |
<td>\gene_symbol_Ensembl*\</td> |
| 3873 |
23 Oct 07 |
nicklas |
350 |
</tr> |
| 3873 |
23 Oct 07 |
nicklas |
351 |
<tr> |
| 3873 |
23 Oct 07 |
nicklas |
352 |
<td><i>Sequence</i></td> |
| 3873 |
23 Oct 07 |
nicklas |
353 |
<td>\oligo_sequence\</td> |
| 3873 |
23 Oct 07 |
nicklas |
354 |
</tr> |
| 3873 |
23 Oct 07 |
nicklas |
355 |
</table> |
| 3873 |
23 Oct 07 |
nicklas |
356 |
|
| 3873 |
23 Oct 07 |
nicklas |
357 |
</td> |
| 3873 |
23 Oct 07 |
nicklas |
358 |
</tr> |
| 3873 |
23 Oct 07 |
nicklas |
359 |
|
| 3873 |
23 Oct 07 |
nicklas |
360 |
<tr class="evenrow"> |
| 3873 |
23 Oct 07 |
nicklas |
361 |
<td>GenePix reporter importer<br>(optional)</td> |
| 3873 |
23 Oct 07 |
nicklas |
362 |
<td>Reporter importer</td> |
| 3873 |
23 Oct 07 |
nicklas |
363 |
<td> |
| 3873 |
23 Oct 07 |
nicklas |
364 |
|
| 3873 |
23 Oct 07 |
nicklas |
365 |
<table border="0" cellspacing="0" cellpadding="2"> |
| 3873 |
23 Oct 07 |
nicklas |
366 |
<tr> |
| 5788 |
06 Oct 11 |
nicklas |
367 |
<td><b>File</b></td> |
| 5788 |
06 Oct 11 |
nicklas |
368 |
<td><code>mouse/<br>genepix.mouse.v4.37k.00h.gpr</code></td> |
| 5788 |
06 Oct 11 |
nicklas |
369 |
</tr> |
| 5788 |
06 Oct 11 |
nicklas |
370 |
<tr> |
| 3873 |
23 Oct 07 |
nicklas |
371 |
<td><i>Data header</i></td> |
| 3873 |
23 Oct 07 |
nicklas |
372 |
<td>"Block"\t"Column"\t"Row"\t"Name"\t"ID"\t.*</td> |
| 3873 |
23 Oct 07 |
nicklas |
373 |
</tr> |
| 3873 |
23 Oct 07 |
nicklas |
374 |
<tr> |
| 3873 |
23 Oct 07 |
nicklas |
375 |
<td><i>Data splitter</i></td> |
| 3873 |
23 Oct 07 |
nicklas |
376 |
<td>\t</td> |
| 3873 |
23 Oct 07 |
nicklas |
377 |
</tr> |
| 3873 |
23 Oct 07 |
nicklas |
378 |
<tr> |
| 3873 |
23 Oct 07 |
nicklas |
379 |
<td><i>Min data columns</i></td> |
| 3873 |
23 Oct 07 |
nicklas |
380 |
<td>48</td> |
| 3873 |
23 Oct 07 |
nicklas |
381 |
</tr> |
| 3873 |
23 Oct 07 |
nicklas |
382 |
<tr> |
| 3873 |
23 Oct 07 |
nicklas |
383 |
<td><i>Max data columns</i></td> |
| 3873 |
23 Oct 07 |
nicklas |
384 |
<td>48</td> |
| 3873 |
23 Oct 07 |
nicklas |
385 |
</tr> |
| 3873 |
23 Oct 07 |
nicklas |
386 |
<tr> |
| 3873 |
23 Oct 07 |
nicklas |
387 |
<td><i>Name</i></td> |
| 3873 |
23 Oct 07 |
nicklas |
388 |
<td>\Name\</td> |
| 3873 |
23 Oct 07 |
nicklas |
389 |
</tr> |
| 3873 |
23 Oct 07 |
nicklas |
390 |
<tr> |
| 4626 |
05 Nov 08 |
nicklas |
391 |
<td><i>External ID</i></td> |
| 3873 |
23 Oct 07 |
nicklas |
392 |
<td>\ID\</td> |
| 3873 |
23 Oct 07 |
nicklas |
393 |
</tr> |
| 3873 |
23 Oct 07 |
nicklas |
394 |
</table> |
| 3873 |
23 Oct 07 |
nicklas |
395 |
|
| 3873 |
23 Oct 07 |
nicklas |
396 |
</td> |
| 3873 |
23 Oct 07 |
nicklas |
397 |
</tr> |
| 3873 |
23 Oct 07 |
nicklas |
398 |
<tr class="oddrow"> |
| 3873 |
23 Oct 07 |
nicklas |
399 |
<td>Reporters from Affymetrix annotations file</td> |
| 3873 |
23 Oct 07 |
nicklas |
400 |
<td>Reporter importer</td> |
| 3873 |
23 Oct 07 |
nicklas |
401 |
<td> |
| 3873 |
23 Oct 07 |
nicklas |
402 |
<table border="0" cellspacing="0" cellpadding="2"> |
| 3873 |
23 Oct 07 |
nicklas |
403 |
<tr> |
| 5788 |
06 Oct 11 |
nicklas |
404 |
<td><b>File</b></td> |
| 5788 |
06 Oct 11 |
nicklas |
405 |
<td><code>affymetrix/annotations/<br>MG_U74Av2_annot.csv.bz2</code></td> |
| 5788 |
06 Oct 11 |
nicklas |
406 |
</tr> |
| 5788 |
06 Oct 11 |
nicklas |
407 |
<tr> |
| 3873 |
23 Oct 07 |
nicklas |
408 |
<td><i>Data header</i></td> |
| 3873 |
23 Oct 07 |
nicklas |
409 |
<td>"Probe Set ID","GeneChip Array".*</td> |
| 3873 |
23 Oct 07 |
nicklas |
410 |
</tr> |
| 3873 |
23 Oct 07 |
nicklas |
411 |
<tr> |
| 3873 |
23 Oct 07 |
nicklas |
412 |
<td><i>Data splitter</i></td> |
| 3873 |
23 Oct 07 |
nicklas |
413 |
<td>(?!"),(?=")</td> |
| 3873 |
23 Oct 07 |
nicklas |
414 |
</tr> |
| 3873 |
23 Oct 07 |
nicklas |
415 |
<tr> |
| 3873 |
23 Oct 07 |
nicklas |
416 |
<td><i>Name</i></td> |
| 3873 |
23 Oct 07 |
nicklas |
417 |
<td>\Probe Set ID\</td> |
| 3873 |
23 Oct 07 |
nicklas |
418 |
</tr> |
| 3873 |
23 Oct 07 |
nicklas |
419 |
<tr> |
| 4626 |
05 Nov 08 |
nicklas |
420 |
<td><i>External ID</i></td> |
| 3873 |
23 Oct 07 |
nicklas |
421 |
<td>\Probe Set ID\</td> |
| 3873 |
23 Oct 07 |
nicklas |
422 |
</tr> |
| 3873 |
23 Oct 07 |
nicklas |
423 |
<tr> |
| 3873 |
23 Oct 07 |
nicklas |
424 |
<td><i>Description</i></td> |
| 3873 |
23 Oct 07 |
nicklas |
425 |
<td>\Target Description\</td> |
| 3873 |
23 Oct 07 |
nicklas |
426 |
</tr> |
| 3873 |
23 Oct 07 |
nicklas |
427 |
<tr> |
| 3873 |
23 Oct 07 |
nicklas |
428 |
<td><i>Gene symbol</i></td> |
| 3873 |
23 Oct 07 |
nicklas |
429 |
<td>\Gene Symbol\</td> |
| 3873 |
23 Oct 07 |
nicklas |
430 |
</tr> |
| 3873 |
23 Oct 07 |
nicklas |
431 |
</table> |
| 3873 |
23 Oct 07 |
nicklas |
432 |
|
| 3873 |
23 Oct 07 |
nicklas |
433 |
</td> |
| 3873 |
23 Oct 07 |
nicklas |
434 |
</tr> |
| 5788 |
06 Oct 11 |
nicklas |
435 |
<tr class="evenrow"> |
| 5788 |
06 Oct 11 |
nicklas |
436 |
<td>Reporters from GTF file</td> |
| 5788 |
06 Oct 11 |
nicklas |
437 |
<td>GTF Reporter importer</td> |
| 5788 |
06 Oct 11 |
nicklas |
438 |
<td> |
| 5788 |
06 Oct 11 |
nicklas |
439 |
|
| 5788 |
06 Oct 11 |
nicklas |
440 |
<table border="0" cellspacing="0" cellpadding="2"> |
| 5788 |
06 Oct 11 |
nicklas |
441 |
<tr> |
| 5788 |
06 Oct 11 |
nicklas |
442 |
<td><b>File</b></td> |
| 5788 |
06 Oct 11 |
nicklas |
443 |
<td><code>sequencing/<br>UCSC_Human_hg19_RefSeqGenes.gtf.tar.bz2</code></td> |
| 5788 |
06 Oct 11 |
nicklas |
444 |
</tr> |
| 5788 |
06 Oct 11 |
nicklas |
445 |
<tr> |
| 5788 |
06 Oct 11 |
nicklas |
446 |
<td><i>Data header</i></td> |
| 5788 |
06 Oct 11 |
nicklas |
447 |
<td><seqname>\t.*<transcript_id>.*</td> |
| 5788 |
06 Oct 11 |
nicklas |
448 |
</tr> |
| 5788 |
06 Oct 11 |
nicklas |
449 |
<tr> |
| 5788 |
06 Oct 11 |
nicklas |
450 |
<td><i>Data splitter</i></td> |
| 5788 |
06 Oct 11 |
nicklas |
451 |
<td>\t</td> |
| 5788 |
06 Oct 11 |
nicklas |
452 |
</tr> |
| 5788 |
06 Oct 11 |
nicklas |
453 |
<tr> |
| 5788 |
06 Oct 11 |
nicklas |
454 |
<td><i>Min data columns</i></td> |
| 5788 |
06 Oct 11 |
nicklas |
455 |
<td>4</td> |
| 5788 |
06 Oct 11 |
nicklas |
456 |
</tr> |
| 5788 |
06 Oct 11 |
nicklas |
457 |
<tr> |
| 5788 |
06 Oct 11 |
nicklas |
458 |
<td><i>Remove quotes</i></td> |
| 5788 |
06 Oct 11 |
nicklas |
459 |
<td>yes</td> |
| 5788 |
06 Oct 11 |
nicklas |
460 |
</tr> |
| 5788 |
06 Oct 11 |
nicklas |
461 |
<tr> |
| 5788 |
06 Oct 11 |
nicklas |
462 |
<td><i>Complex mappings</i></td> |
| 5788 |
06 Oct 11 |
nicklas |
463 |
<td>allow</td> |
| 5788 |
06 Oct 11 |
nicklas |
464 |
</tr> |
| 5788 |
06 Oct 11 |
nicklas |
465 |
<tr> |
| 5788 |
06 Oct 11 |
nicklas |
466 |
<td><i>Name</i></td> |
| 5788 |
06 Oct 11 |
nicklas |
467 |
<td>\<transcript_id>\@\<seqname>\</td> |
| 5788 |
06 Oct 11 |
nicklas |
468 |
</tr> |
| 5788 |
06 Oct 11 |
nicklas |
469 |
<tr> |
| 5788 |
06 Oct 11 |
nicklas |
470 |
<td><i>External ID</i></td> |
| 5788 |
06 Oct 11 |
nicklas |
471 |
<td>\<transcript_id>\@\<seqname>\</td> |
| 5788 |
06 Oct 11 |
nicklas |
472 |
</tr> |
| 5788 |
06 Oct 11 |
nicklas |
473 |
<tr> |
| 5788 |
06 Oct 11 |
nicklas |
474 |
<td><i>Gene symbol</i></td> |
| 5788 |
06 Oct 11 |
nicklas |
475 |
<td>\<gene_id>\</td> |
| 5788 |
06 Oct 11 |
nicklas |
476 |
</tr> |
| 5788 |
06 Oct 11 |
nicklas |
477 |
<tr> |
| 5788 |
06 Oct 11 |
nicklas |
478 |
<td><i>Chromosome</i></td> |
| 5788 |
06 Oct 11 |
nicklas |
479 |
<td>\<seqname>\</td> |
| 5788 |
06 Oct 11 |
nicklas |
480 |
</tr> |
| 5788 |
06 Oct 11 |
nicklas |
481 |
</table> |
| 5788 |
06 Oct 11 |
nicklas |
482 |
|
| 5788 |
06 Oct 11 |
nicklas |
483 |
</td> |
| 5788 |
06 Oct 11 |
nicklas |
484 |
</tr> |
| 3873 |
23 Oct 07 |
nicklas |
485 |
</table> |
| 4013 |
28 Nov 07 |
nicklas |
486 |
<p> |
| 3873 |
23 Oct 07 |
nicklas |
487 |
</li> |
| 3873 |
23 Oct 07 |
nicklas |
488 |
|
| 4013 |
28 Nov 07 |
nicklas |
489 |
<li> |
| 4013 |
28 Nov 07 |
nicklas |
490 |
Import reporters: |
| 4013 |
28 Nov 07 |
nicklas |
491 |
<ol> |
| 4013 |
28 Nov 07 |
nicklas |
492 |
<li>Go to the <code>View -> Reporters</code> page.</li> |
| 4013 |
28 Nov 07 |
nicklas |
493 |
<li>Click on the <code>Import</code> button.</li> |
| 4013 |
28 Nov 07 |
nicklas |
494 |
<li>Choose <code>auto-detect</code> and then upload |
| 4013 |
28 Nov 07 |
nicklas |
495 |
the file <code>plates_and_reporters.mouse.v4.37k.txt</code>.</li> |
| 4013 |
28 Nov 07 |
nicklas |
496 |
<li>The <code>Reporters for project A</code> format should be |
| 4013 |
28 Nov 07 |
nicklas |
497 |
found.</li> |
| 4013 |
28 Nov 07 |
nicklas |
498 |
<li>Select the <code>skip</code> option for the "Missing a required" value |
| 4013 |
28 Nov 07 |
nicklas |
499 |
since the file contains rows with empty reporter ID:s. |
| 4013 |
28 Nov 07 |
nicklas |
500 |
<li>Continue and wait for the import to finish. It should create 35,912 new reporters.</li> |
| 4013 |
28 Nov 07 |
nicklas |
501 |
<li> |
| 4013 |
28 Nov 07 |
nicklas |
502 |
Repeat the procedure with the <code>MG_U74Av2_annot.csv</code> file. This time |
| 4013 |
28 Nov 07 |
nicklas |
503 |
also select <code>crop</code> for the "String too long" setting since |
| 4013 |
28 Nov 07 |
nicklas |
504 |
the file contains data that is too large for the datbase. |
| 4013 |
28 Nov 07 |
nicklas |
505 |
12,488 new reporters should be created. |
| 5788 |
06 Oct 11 |
nicklas |
506 |
<li> |
| 5788 |
06 Oct 11 |
nicklas |
507 |
Repeat the procedure with the <code>UCSC_Human_hg19_RefSeqGenes.gtf</code> |
| 5788 |
06 Oct 11 |
nicklas |
508 |
file. The default error handling options can be used. This time |
| 5788 |
06 Oct 11 |
nicklas |
509 |
38,977 new reporters should be created. |
| 4013 |
28 Nov 07 |
nicklas |
510 |
</ol> |
| 4013 |
28 Nov 07 |
nicklas |
511 |
<p> |
| 4013 |
28 Nov 07 |
nicklas |
512 |
|
| 4013 |
28 Nov 07 |
nicklas |
513 |
</li> |
| 4013 |
28 Nov 07 |
nicklas |
514 |
|
| 4013 |
28 Nov 07 |
nicklas |
515 |
|
| 2568 |
22 Aug 06 |
nicklas |
516 |
</ol> |
| 2568 |
22 Aug 06 |
nicklas |
517 |
|
| 2568 |
22 Aug 06 |
nicklas |
518 |
|
| 2568 |
22 Aug 06 |
nicklas |
519 |
<a name="power"></a> |
| 2568 |
22 Aug 06 |
nicklas |
520 |
<h2>4. Power user tests</h2> |
| 2568 |
22 Aug 06 |
nicklas |
521 |
<p> |
| 2682 |
02 Oct 06 |
jari |
522 |
The power user is the typical owner/administrator of a project. The power user sets |
| 2568 |
22 Aug 06 |
nicklas |
523 |
up common resources used in the project, such as hardware, software, protocols, |
| 2568 |
22 Aug 06 |
nicklas |
524 |
file formats and annotation types. In this case the power user is also responsible for |
| 2568 |
22 Aug 06 |
nicklas |
525 |
managing the LIMS. |
| 2568 |
22 Aug 06 |
nicklas |
526 |
</p> |
| 2568 |
22 Aug 06 |
nicklas |
527 |
|
| 2568 |
22 Aug 06 |
nicklas |
528 |
<ol> |
| 2568 |
22 Aug 06 |
nicklas |
529 |
<li> |
| 2568 |
22 Aug 06 |
nicklas |
530 |
Create a project: |
| 2568 |
22 Aug 06 |
nicklas |
531 |
|
| 2568 |
22 Aug 06 |
nicklas |
532 |
<table class="listing" cellspacing="0" cellpadding="2" border="0"> |
| 2568 |
22 Aug 06 |
nicklas |
533 |
<tr> |
| 2568 |
22 Aug 06 |
nicklas |
534 |
<th>Name</th> |
| 2568 |
22 Aug 06 |
nicklas |
535 |
<th>Members</th> |
| 2568 |
22 Aug 06 |
nicklas |
536 |
</tr> |
| 2568 |
22 Aug 06 |
nicklas |
537 |
<tr> |
| 2568 |
22 Aug 06 |
nicklas |
538 |
<td>Project A</td> |
| 2568 |
22 Aug 06 |
nicklas |
539 |
<td>Groups: Group A (Use permission)</td> |
| 2568 |
22 Aug 06 |
nicklas |
540 |
</tr> |
| 2568 |
22 Aug 06 |
nicklas |
541 |
</table> |
| 2568 |
22 Aug 06 |
nicklas |
542 |
<p> |
| 2568 |
22 Aug 06 |
nicklas |
543 |
</li> |
| 2568 |
22 Aug 06 |
nicklas |
544 |
|
| 2568 |
22 Aug 06 |
nicklas |
545 |
<li>Activate the project.<p></li> |
| 2568 |
22 Aug 06 |
nicklas |
546 |
|
| 2568 |
22 Aug 06 |
nicklas |
547 |
<li> |
| 5144 |
20 Oct 09 |
nicklas |
548 |
Create annotation types [A] and protocol parameters [P]: |
| 5144 |
20 Oct 09 |
nicklas |
549 |
<table class="listing" cellspacing="0" cellpadding="2" border="0"> |
| 5144 |
20 Oct 09 |
nicklas |
550 |
<tr> |
| 5144 |
20 Oct 09 |
nicklas |
551 |
<th>Name</th> |
| 5144 |
20 Oct 09 |
nicklas |
552 |
<th>Type</th> |
| 5144 |
20 Oct 09 |
nicklas |
553 |
<th>Unit</th> |
| 5144 |
20 Oct 09 |
nicklas |
554 |
<th>Interface</th> |
| 5144 |
20 Oct 09 |
nicklas |
555 |
<th>Values</th> |
| 5144 |
20 Oct 09 |
nicklas |
556 |
<th>Item types</th> |
| 5144 |
20 Oct 09 |
nicklas |
557 |
</tr> |
| 5144 |
20 Oct 09 |
nicklas |
558 |
<tr> |
| 5144 |
20 Oct 09 |
nicklas |
559 |
<td>Drug resistance [A]</td> |
| 5144 |
20 Oct 09 |
nicklas |
560 |
<td>String</td> |
| 5144 |
20 Oct 09 |
nicklas |
561 |
<td>-</td> |
| 5144 |
20 Oct 09 |
nicklas |
562 |
<td>radiobuttons</td> |
| 5144 |
20 Oct 09 |
nicklas |
563 |
<td>high, medium, low</td> |
| 5144 |
20 Oct 09 |
nicklas |
564 |
<td>Biosource</td> |
| 5144 |
20 Oct 09 |
nicklas |
565 |
</tr> |
| 5144 |
20 Oct 09 |
nicklas |
566 |
<tr> |
| 5144 |
20 Oct 09 |
nicklas |
567 |
<td>Time [A]</td> |
| 5144 |
20 Oct 09 |
nicklas |
568 |
<td>Integer</td> |
| 5144 |
20 Oct 09 |
nicklas |
569 |
<td>Hour</td> |
| 5144 |
20 Oct 09 |
nicklas |
570 |
<td>text box</td> |
| 5144 |
20 Oct 09 |
nicklas |
571 |
<td>-</td> |
| 5144 |
20 Oct 09 |
nicklas |
572 |
<td>Sample</td> |
| 5144 |
20 Oct 09 |
nicklas |
573 |
</tr> |
| 5144 |
20 Oct 09 |
nicklas |
574 |
<tr> |
| 5983 |
23 Feb 12 |
nicklas |
575 |
<td>RIN [A]</td> |
| 5983 |
23 Feb 12 |
nicklas |
576 |
<td>Float</td> |
| 5983 |
23 Feb 12 |
nicklas |
577 |
<td>-</td> |
| 5983 |
23 Feb 12 |
nicklas |
578 |
<td>text box</td> |
| 5983 |
23 Feb 12 |
nicklas |
579 |
<td>-</td> |
| 5983 |
23 Feb 12 |
nicklas |
580 |
<td>Extract</td> |
| 5983 |
23 Feb 12 |
nicklas |
581 |
</tr> |
| 5983 |
23 Feb 12 |
nicklas |
582 |
<tr> |
| 5144 |
20 Oct 09 |
nicklas |
583 |
<td>Dye swap [A]</td> |
| 5144 |
20 Oct 09 |
nicklas |
584 |
<td>Boolean</td> |
| 5144 |
20 Oct 09 |
nicklas |
585 |
<td>-</td> |
| 5144 |
20 Oct 09 |
nicklas |
586 |
<td>-</td> |
| 5144 |
20 Oct 09 |
nicklas |
587 |
<td>-</td> |
| 5144 |
20 Oct 09 |
nicklas |
588 |
<td>Raw bioassay</td> |
| 5144 |
20 Oct 09 |
nicklas |
589 |
</tr> |
| 5144 |
20 Oct 09 |
nicklas |
590 |
<tr> |
| 5144 |
20 Oct 09 |
nicklas |
591 |
<td>PMT gain [P]</td> |
| 5144 |
20 Oct 09 |
nicklas |
592 |
<td>Float</td> |
| 5144 |
20 Oct 09 |
nicklas |
593 |
<td>Volt (Electric potential)</td> |
| 5144 |
20 Oct 09 |
nicklas |
594 |
<td>-</td> |
| 5144 |
20 Oct 09 |
nicklas |
595 |
<td>-</td> |
| 5788 |
06 Oct 11 |
nicklas |
596 |
<td>Derived bioassay</td> |
| 5144 |
20 Oct 09 |
nicklas |
597 |
</tr> |
| 5144 |
20 Oct 09 |
nicklas |
598 |
</table> |
| 5144 |
20 Oct 09 |
nicklas |
599 |
<p> |
| 5144 |
20 Oct 09 |
nicklas |
600 |
</li> |
| 5144 |
20 Oct 09 |
nicklas |
601 |
|
| 5144 |
20 Oct 09 |
nicklas |
602 |
<li> |
| 5983 |
23 Feb 12 |
nicklas |
603 |
Create item subtypes: |
| 5983 |
23 Feb 12 |
nicklas |
604 |
<table class="listing" cellspacing="0" cellpadding="2" border="0"> |
| 5983 |
23 Feb 12 |
nicklas |
605 |
<tr> |
| 5983 |
23 Feb 12 |
nicklas |
606 |
<th>Name</th> |
| 5983 |
23 Feb 12 |
nicklas |
607 |
<th>Item type</th> |
| 5983 |
23 Feb 12 |
nicklas |
608 |
<th>Push annotations to parent</th> |
| 5983 |
23 Feb 12 |
nicklas |
609 |
</tr> |
| 5983 |
23 Feb 12 |
nicklas |
610 |
<tr> |
| 5983 |
23 Feb 12 |
nicklas |
611 |
<td>Quality control</td> |
| 5983 |
23 Feb 12 |
nicklas |
612 |
<td>Extract</td> |
| 5983 |
23 Feb 12 |
nicklas |
613 |
<td>Yes</td> |
| 5983 |
23 Feb 12 |
nicklas |
614 |
</tr> |
| 5983 |
23 Feb 12 |
nicklas |
615 |
</table> |
| 5983 |
23 Feb 12 |
nicklas |
616 |
<p> |
| 5983 |
23 Feb 12 |
nicklas |
617 |
</li> |
| 5983 |
23 Feb 12 |
nicklas |
618 |
|
| 5983 |
23 Feb 12 |
nicklas |
619 |
<li> |
| 6124 |
13 Sep 12 |
nicklas |
620 |
Create protocols (keep the 'Add as project default' option checked and the 'Replace existing default' unchecked): |
| 2568 |
22 Aug 06 |
nicklas |
621 |
<table class="listing" cellspacing="0" cellpadding="2" border="0"> |
| 2568 |
22 Aug 06 |
nicklas |
622 |
<tr> |
| 2568 |
22 Aug 06 |
nicklas |
623 |
<th>Name</th> |
| 2568 |
22 Aug 06 |
nicklas |
624 |
<th>Type</th> |
| 5144 |
20 Oct 09 |
nicklas |
625 |
<th>Comment</th> |
| 2568 |
22 Aug 06 |
nicklas |
626 |
</tr> |
| 2568 |
22 Aug 06 |
nicklas |
627 |
<tr> |
| 2568 |
22 Aug 06 |
nicklas |
628 |
<td>Sampling A</td> |
| 2568 |
22 Aug 06 |
nicklas |
629 |
<td>Sampling</td> |
| 2568 |
22 Aug 06 |
nicklas |
630 |
</tr> |
| 2568 |
22 Aug 06 |
nicklas |
631 |
<tr> |
| 2568 |
22 Aug 06 |
nicklas |
632 |
<td>Extraction A</td> |
| 2568 |
22 Aug 06 |
nicklas |
633 |
<td>Extraction</td> |
| 2568 |
22 Aug 06 |
nicklas |
634 |
</tr> |
| 2568 |
22 Aug 06 |
nicklas |
635 |
<tr> |
| 2568 |
22 Aug 06 |
nicklas |
636 |
<td>Labeling A</td> |
| 2568 |
22 Aug 06 |
nicklas |
637 |
<td>Labeling</td> |
| 2568 |
22 Aug 06 |
nicklas |
638 |
</tr> |
| 2568 |
22 Aug 06 |
nicklas |
639 |
<tr> |
| 5699 |
16 Aug 11 |
nicklas |
640 |
<td>Library preparation A</td> |
| 5699 |
16 Aug 11 |
nicklas |
641 |
<td>Library preparation</td> |
| 5699 |
16 Aug 11 |
nicklas |
642 |
</tr> |
| 5699 |
16 Aug 11 |
nicklas |
643 |
<tr> |
| 2568 |
22 Aug 06 |
nicklas |
644 |
<td>Hybridization A</td> |
| 2568 |
22 Aug 06 |
nicklas |
645 |
<td>Hybridization</td> |
| 2568 |
22 Aug 06 |
nicklas |
646 |
</tr> |
| 2568 |
22 Aug 06 |
nicklas |
647 |
<tr> |
| 5699 |
16 Aug 11 |
nicklas |
648 |
<td>cBot Settings A</td> |
| 5699 |
16 Aug 11 |
nicklas |
649 |
<td>Cluster generation</td> |
| 5699 |
16 Aug 11 |
nicklas |
650 |
</tr> |
| 5699 |
16 Aug 11 |
nicklas |
651 |
<tr> |
| 2568 |
22 Aug 06 |
nicklas |
652 |
<td>Scanning A</td> |
| 2568 |
22 Aug 06 |
nicklas |
653 |
<td>Scanning</td> |
| 5144 |
20 Oct 09 |
nicklas |
654 |
<td>Select 'PMT gain' as a protocol parameter.</td> |
| 2568 |
22 Aug 06 |
nicklas |
655 |
</tr> |
| 2568 |
22 Aug 06 |
nicklas |
656 |
<tr> |
| 5699 |
16 Aug 11 |
nicklas |
657 |
<td>HiSeq Settings A</td> |
| 5699 |
16 Aug 11 |
nicklas |
658 |
<td>Sequencing</td> |
| 5699 |
16 Aug 11 |
nicklas |
659 |
</tr> |
| 5699 |
16 Aug 11 |
nicklas |
660 |
<tr> |
| 5699 |
16 Aug 11 |
nicklas |
661 |
<td>TopHat Settings A</td> |
| 5699 |
16 Aug 11 |
nicklas |
662 |
<td>Alignment</td> |
| 5699 |
16 Aug 11 |
nicklas |
663 |
</tr> |
| 5699 |
16 Aug 11 |
nicklas |
664 |
<tr> |
| 2568 |
22 Aug 06 |
nicklas |
665 |
<td>Feature extraction A</td> |
| 2568 |
22 Aug 06 |
nicklas |
666 |
<td>Feature extraction</td> |
| 2568 |
22 Aug 06 |
nicklas |
667 |
</tr> |
| 2568 |
22 Aug 06 |
nicklas |
668 |
<tr> |
| 5699 |
16 Aug 11 |
nicklas |
669 |
<td>Cufflinks Settings A</td> |
| 5699 |
16 Aug 11 |
nicklas |
670 |
<td>Feature extraction</td> |
| 5699 |
16 Aug 11 |
nicklas |
671 |
</tr> |
| 5699 |
16 Aug 11 |
nicklas |
672 |
<tr> |
| 2568 |
22 Aug 06 |
nicklas |
673 |
<td>Printing A</td> |
| 2568 |
22 Aug 06 |
nicklas |
674 |
<td>Printing</td> |
| 2568 |
22 Aug 06 |
nicklas |
675 |
</tr> |
| 2568 |
22 Aug 06 |
nicklas |
676 |
</table> |
| 2568 |
22 Aug 06 |
nicklas |
677 |
<p> |
| 2568 |
22 Aug 06 |
nicklas |
678 |
</li> |
| 2568 |
22 Aug 06 |
nicklas |
679 |
|
| 2568 |
22 Aug 06 |
nicklas |
680 |
<li> |
| 6124 |
13 Sep 12 |
nicklas |
681 |
Create hardware (keep the 'Add as project default' option checked and the 'Replace existing default' unchecked): |
| 2568 |
22 Aug 06 |
nicklas |
682 |
<table class="listing" cellspacing="0" cellpadding="2" border="0"> |
| 2568 |
22 Aug 06 |
nicklas |
683 |
<tr> |
| 2568 |
22 Aug 06 |
nicklas |
684 |
<th>Name</th> |
| 2568 |
22 Aug 06 |
nicklas |
685 |
<th>Type</th> |
| 2568 |
22 Aug 06 |
nicklas |
686 |
</tr> |
| 2568 |
22 Aug 06 |
nicklas |
687 |
<tr> |
| 2568 |
22 Aug 06 |
nicklas |
688 |
<td>Hybridization station A</td> |
| 2568 |
22 Aug 06 |
nicklas |
689 |
<td>Hybridization station</td> |
| 2568 |
22 Aug 06 |
nicklas |
690 |
</tr> |
| 2568 |
22 Aug 06 |
nicklas |
691 |
<tr> |
| 5699 |
16 Aug 11 |
nicklas |
692 |
<td>cBot A</td> |
| 5699 |
16 Aug 11 |
nicklas |
693 |
<td>Cluster generator</td> |
| 5699 |
16 Aug 11 |
nicklas |
694 |
</tr> |
| 5699 |
16 Aug 11 |
nicklas |
695 |
<tr> |
| 5699 |
16 Aug 11 |
nicklas |
696 |
<td>HiSeq 2000 A</td> |
| 5699 |
16 Aug 11 |
nicklas |
697 |
<td>Sequencer</td> |
| 5699 |
16 Aug 11 |
nicklas |
698 |
</tr> |
| 5699 |
16 Aug 11 |
nicklas |
699 |
<tr> |
| 2568 |
22 Aug 06 |
nicklas |
700 |
<td>Scanner A</td> |
| 2568 |
22 Aug 06 |
nicklas |
701 |
<td>Scanner</td> |
| 2568 |
22 Aug 06 |
nicklas |
702 |
</tr> |
| 2568 |
22 Aug 06 |
nicklas |
703 |
<tr> |
| 2568 |
22 Aug 06 |
nicklas |
704 |
<td>Print robot A</td> |
| 2568 |
22 Aug 06 |
nicklas |
705 |
<td>Print robot</td> |
| 2568 |
22 Aug 06 |
nicklas |
706 |
</tr> |
| 2568 |
22 Aug 06 |
nicklas |
707 |
</table> |
| 2568 |
22 Aug 06 |
nicklas |
708 |
<p> |
| 2568 |
22 Aug 06 |
nicklas |
709 |
</li> |
| 2568 |
22 Aug 06 |
nicklas |
710 |
|
| 2568 |
22 Aug 06 |
nicklas |
711 |
<li> |
| 6124 |
13 Sep 12 |
nicklas |
712 |
Create software (keep the 'Add as project default' option checked and the 'Replace existing default' unchecked): |
| 2568 |
22 Aug 06 |
nicklas |
713 |
<table class="listing" cellspacing="0" cellpadding="2" border="0"> |
| 2568 |
22 Aug 06 |
nicklas |
714 |
<tr> |
| 2568 |
22 Aug 06 |
nicklas |
715 |
<th>Name</th> |
| 2568 |
22 Aug 06 |
nicklas |
716 |
<th>Type</th> |
| 2568 |
22 Aug 06 |
nicklas |
717 |
</tr> |
| 2568 |
22 Aug 06 |
nicklas |
718 |
<tr> |
| 2568 |
22 Aug 06 |
nicklas |
719 |
<td>Software A</td> |
| 2568 |
22 Aug 06 |
nicklas |
720 |
<td>Feature extraction</td> |
| 2568 |
22 Aug 06 |
nicklas |
721 |
</tr> |
| 2568 |
22 Aug 06 |
nicklas |
722 |
</table> |
| 2568 |
22 Aug 06 |
nicklas |
723 |
<p> |
| 2568 |
22 Aug 06 |
nicklas |
724 |
</li> |
| 5886 |
23 Nov 11 |
nicklas |
725 |
|
| 5886 |
23 Nov 11 |
nicklas |
726 |
<li> |
| 5886 |
23 Nov 11 |
nicklas |
727 |
Create a reporter clone template: |
| 5886 |
23 Nov 11 |
nicklas |
728 |
<table class="listing" cellspacing="0" cellpadding="2" border="0"> |
| 5886 |
23 Nov 11 |
nicklas |
729 |
<tr> |
| 5886 |
23 Nov 11 |
nicklas |
730 |
<th>Name</th> |
| 5886 |
23 Nov 11 |
nicklas |
731 |
<th>Properties</th> |
| 5886 |
23 Nov 11 |
nicklas |
732 |
</tr> |
| 5886 |
23 Nov 11 |
nicklas |
733 |
<tr> |
| 5886 |
23 Nov 11 |
nicklas |
734 |
<td>Template A</td> |
| 5886 |
23 Nov 11 |
nicklas |
735 |
<td>External ID, ID, Version, Sequence, Gene symbol</td> |
| 5886 |
23 Nov 11 |
nicklas |
736 |
</tr> |
| 5886 |
23 Nov 11 |
nicklas |
737 |
</table> |
| 5886 |
23 Nov 11 |
nicklas |
738 |
<p> |
| 5886 |
23 Nov 11 |
nicklas |
739 |
</li> |
| 2568 |
22 Aug 06 |
nicklas |
740 |
|
| 2568 |
22 Aug 06 |
nicklas |
741 |
<li> |
| 5260 |
04 Mar 10 |
nicklas |
742 |
Create bioplate type: |
| 5260 |
04 Mar 10 |
nicklas |
743 |
<table class="listing" cellspacing="0" cellpadding="2" border="0"> |
| 5260 |
04 Mar 10 |
nicklas |
744 |
<tr> |
| 5260 |
04 Mar 10 |
nicklas |
745 |
<th>Name</th> |
| 5260 |
04 Mar 10 |
nicklas |
746 |
<th>Biomaterial type</th> |
| 5474 |
03 Nov 10 |
nicklas |
747 |
<th>Well lock mode</th> |
| 5260 |
04 Mar 10 |
nicklas |
748 |
</tr> |
| 5260 |
04 Mar 10 |
nicklas |
749 |
<tr> |
| 5260 |
04 Mar 10 |
nicklas |
750 |
<td>Bioplate type A</td> |
| 5474 |
03 Nov 10 |
nicklas |
751 |
<td>Any</td> |
| 5474 |
03 Nov 10 |
nicklas |
752 |
<td>Unlocked</td> |
| 5260 |
04 Mar 10 |
nicklas |
753 |
</tr> |
| 5260 |
04 Mar 10 |
nicklas |
754 |
</table> |
| 5260 |
04 Mar 10 |
nicklas |
755 |
<p> |
| 5260 |
04 Mar 10 |
nicklas |
756 |
</li> |
| 5260 |
04 Mar 10 |
nicklas |
757 |
|
| 5260 |
04 Mar 10 |
nicklas |
758 |
<li> |
| 2682 |
02 Oct 06 |
jari |
759 |
Create file formats (<i>i.e.</i>, plug-in configurations). The formats marked as |
| 2568 |
22 Aug 06 |
nicklas |
760 |
optional are not used in the test procedure, but may be useful to weed |
| 2568 |
22 Aug 06 |
nicklas |
761 |
out import problems, since they allow importing all info from the raw |
| 2751 |
20 Oct 06 |
nicklas |
762 |
data files. You may either enter the regular expressions as specified or |
| 2751 |
20 Oct 06 |
nicklas |
763 |
use the "Test with file" feature. |
| 2568 |
22 Aug 06 |
nicklas |
764 |
|
| 2568 |
22 Aug 06 |
nicklas |
765 |
<table class="listing" cellspacing="0" cellpadding="2" border="0"> |
| 2568 |
22 Aug 06 |
nicklas |
766 |
<tr> |
| 2568 |
22 Aug 06 |
nicklas |
767 |
<th>Name</th> |
| 2568 |
22 Aug 06 |
nicklas |
768 |
<th>Plugin</th> |
| 2568 |
22 Aug 06 |
nicklas |
769 |
<th>Configuration values</th> |
| 2568 |
22 Aug 06 |
nicklas |
770 |
</tr> |
| 2568 |
22 Aug 06 |
nicklas |
771 |
|
| 2568 |
22 Aug 06 |
nicklas |
772 |
<tr class="oddrow"> |
| 2568 |
22 Aug 06 |
nicklas |
773 |
<td>Plates for project A</td> |
| 2568 |
22 Aug 06 |
nicklas |
774 |
<td>Plate importer</td> |
| 2568 |
22 Aug 06 |
nicklas |
775 |
<td> |
| 2568 |
22 Aug 06 |
nicklas |
776 |
|
| 2568 |
22 Aug 06 |
nicklas |
777 |
<table border="0" cellspacing="0" cellpadding="2"> |
| 2568 |
22 Aug 06 |
nicklas |
778 |
<tr> |
| 5788 |
06 Oct 11 |
nicklas |
779 |
<td><b>File</b></td> |
| 5788 |
06 Oct 11 |
nicklas |
780 |
<td><code>mouse/<br>plates_and_reporters.mouse.v4.37k.txt</code></td> |
| 5788 |
06 Oct 11 |
nicklas |
781 |
</tr> |
| 5788 |
06 Oct 11 |
nicklas |
782 |
<tr> |
| 2568 |
22 Aug 06 |
nicklas |
783 |
<td><i>Data header</i></td> |
| 2568 |
22 Aug 06 |
nicklas |
784 |
<td>384_number\t384_column\t384_row\t384_position\toligo_id.*</td> |
| 2568 |
22 Aug 06 |
nicklas |
785 |
</tr> |
| 2568 |
22 Aug 06 |
nicklas |
786 |
<tr> |
| 2568 |
22 Aug 06 |
nicklas |
787 |
<td><i>Data splitter</i></td> |
| 2568 |
22 Aug 06 |
nicklas |
788 |
<td>\t</td> |
| 2568 |
22 Aug 06 |
nicklas |
789 |
</tr> |
| 2568 |
22 Aug 06 |
nicklas |
790 |
<tr> |
| 2568 |
22 Aug 06 |
nicklas |
791 |
<td><i>Min data columns</i></td> |
| 2568 |
22 Aug 06 |
nicklas |
792 |
<td>5</td> |
| 2568 |
22 Aug 06 |
nicklas |
793 |
</tr> |
| 2568 |
22 Aug 06 |
nicklas |
794 |
<tr> |
| 2568 |
22 Aug 06 |
nicklas |
795 |
<td><i>Plate number/name</i></td> |
| 2568 |
22 Aug 06 |
nicklas |
796 |
<td>\384_number\</td> |
| 2568 |
22 Aug 06 |
nicklas |
797 |
</tr> |
| 2568 |
22 Aug 06 |
nicklas |
798 |
<tr> |
| 2568 |
22 Aug 06 |
nicklas |
799 |
<td><i>Row</i></td> |
| 2568 |
22 Aug 06 |
nicklas |
800 |
<td>\384_row\</td> |
| 2568 |
22 Aug 06 |
nicklas |
801 |
</tr> |
| 2568 |
22 Aug 06 |
nicklas |
802 |
<tr> |
| 2568 |
22 Aug 06 |
nicklas |
803 |
<td><i>Column</i></td> |
| 2568 |
22 Aug 06 |
nicklas |
804 |
<td>\384_column\</td> |
| 2568 |
22 Aug 06 |
nicklas |
805 |
</tr> |
| 2568 |
22 Aug 06 |
nicklas |
806 |
<tr> |
| 2568 |
22 Aug 06 |
nicklas |
807 |
<td><i>Reporter ID</i></td> |
| 2568 |
22 Aug 06 |
nicklas |
808 |
<td>\oligo_id\</td> |
| 2568 |
22 Aug 06 |
nicklas |
809 |
</tr> |
| 2568 |
22 Aug 06 |
nicklas |
810 |
</table> |
| 2568 |
22 Aug 06 |
nicklas |
811 |
|
| 2568 |
22 Aug 06 |
nicklas |
812 |
</td> |
| 2568 |
22 Aug 06 |
nicklas |
813 |
</tr> |
| 2568 |
22 Aug 06 |
nicklas |
814 |
|
| 2568 |
22 Aug 06 |
nicklas |
815 |
<tr class="evenrow"> |
| 2568 |
22 Aug 06 |
nicklas |
816 |
<td>GenePix feature importer<br>(optional)</td> |
| 2568 |
22 Aug 06 |
nicklas |
817 |
<td>Reporter map importer</td> |
| 2568 |
22 Aug 06 |
nicklas |
818 |
<td> |
| 2568 |
22 Aug 06 |
nicklas |
819 |
|
| 2568 |
22 Aug 06 |
nicklas |
820 |
<table border="0" cellspacing="0" cellpadding="2"> |
| 2568 |
22 Aug 06 |
nicklas |
821 |
<tr> |
| 5788 |
06 Oct 11 |
nicklas |
822 |
<td><b>File</b></td> |
| 5788 |
06 Oct 11 |
nicklas |
823 |
<td><code>mouse/<br>genepix.mouse.v4.37k.00h.gpr</code></td> |
| 5788 |
06 Oct 11 |
nicklas |
824 |
</tr> |
| 5788 |
06 Oct 11 |
nicklas |
825 |
<tr> |
| 2568 |
22 Aug 06 |
nicklas |
826 |
<td><i>Data header</i></td> |
| 2568 |
22 Aug 06 |
nicklas |
827 |
<td>"Block"\t"Column"\t"Row"\t"Name"\t"ID"\t.*</td> |
| 2568 |
22 Aug 06 |
nicklas |
828 |
</tr> |
| 2568 |
22 Aug 06 |
nicklas |
829 |
<tr> |
| 2568 |
22 Aug 06 |
nicklas |
830 |
<td><i>Data splitter</i></td> |
| 2568 |
22 Aug 06 |
nicklas |
831 |
<td>\t</td> |
| 2568 |
22 Aug 06 |
nicklas |
832 |
</tr> |
| 2568 |
22 Aug 06 |
nicklas |
833 |
<tr> |
| 2568 |
22 Aug 06 |
nicklas |
834 |
<td><i>Min data columns</i></td> |
| 2568 |
22 Aug 06 |
nicklas |
835 |
<td>48</td> |
| 2568 |
22 Aug 06 |
nicklas |
836 |
</tr> |
| 2568 |
22 Aug 06 |
nicklas |
837 |
<tr> |
| 2568 |
22 Aug 06 |
nicklas |
838 |
<td><i>Max data columns</i></td> |
| 2568 |
22 Aug 06 |
nicklas |
839 |
<td>48</td> |
| 2568 |
22 Aug 06 |
nicklas |
840 |
</tr> |
| 2568 |
22 Aug 06 |
nicklas |
841 |
<tr> |
| 2568 |
22 Aug 06 |
nicklas |
842 |
<td><i>Reporter ID</i></td> |
| 2568 |
22 Aug 06 |
nicklas |
843 |
<td>\ID\</td> |
| 2568 |
22 Aug 06 |
nicklas |
844 |
</tr> |
| 2568 |
22 Aug 06 |
nicklas |
845 |
<tr> |
| 2568 |
22 Aug 06 |
nicklas |
846 |
<td><i>Block</i></td> |
| 2568 |
22 Aug 06 |
nicklas |
847 |
<td>\Block\</td> |
| 2568 |
22 Aug 06 |
nicklas |
848 |
</tr> |
| 2568 |
22 Aug 06 |
nicklas |
849 |
<tr> |
| 2568 |
22 Aug 06 |
nicklas |
850 |
<td><i>Column</i></td> |
| 2568 |
22 Aug 06 |
nicklas |
851 |
<td>\Column\</td> |
| 2568 |
22 Aug 06 |
nicklas |
852 |
</tr> |
| 2568 |
22 Aug 06 |
nicklas |
853 |
<tr> |
| 2568 |
22 Aug 06 |
nicklas |
854 |
<td><i>Row</i></td> |
| 2568 |
22 Aug 06 |
nicklas |
855 |
<td>\Row\</td> |
| 2568 |
22 Aug 06 |
nicklas |
856 |
</tr> |
| 2568 |
22 Aug 06 |
nicklas |
857 |
</table> |
| 2568 |
22 Aug 06 |
nicklas |
858 |
|
| 2568 |
22 Aug 06 |
nicklas |
859 |
</td> |
| 2568 |
22 Aug 06 |
nicklas |
860 |
</tr> |
| 2568 |
22 Aug 06 |
nicklas |
861 |
|
| 2568 |
22 Aug 06 |
nicklas |
862 |
<tr class="oddrow"> |
| 5788 |
06 Oct 11 |
nicklas |
863 |
<td>GTF features for project A</td> |
| 5788 |
06 Oct 11 |
nicklas |
864 |
<td>GTF reporter map importer</td> |
| 5788 |
06 Oct 11 |
nicklas |
865 |
<td> |
| 5788 |
06 Oct 11 |
nicklas |
866 |
|
| 5788 |
06 Oct 11 |
nicklas |
867 |
<table border="0" cellspacing="0" cellpadding="2"> |
| 5788 |
06 Oct 11 |
nicklas |
868 |
<tr> |
| 5788 |
06 Oct 11 |
nicklas |
869 |
<td><b>File</b></td> |
| 5788 |
06 Oct 11 |
nicklas |
870 |
<td><code>sequencing/<br>UCSC_Human_hg19_RefSeqGenes.gtf</code></td> |
| 5788 |
06 Oct 11 |
nicklas |
871 |
</tr> |
| 5788 |
06 Oct 11 |
nicklas |
872 |
<tr> |
| 5788 |
06 Oct 11 |
nicklas |
873 |
<td><i>Data header</i></td> |
| 5788 |
06 Oct 11 |
nicklas |
874 |
<td><seqname>\t.*<transcript_id>.*</td> |
| 5788 |
06 Oct 11 |
nicklas |
875 |
</tr> |
| 5788 |
06 Oct 11 |
nicklas |
876 |
<tr> |
| 5788 |
06 Oct 11 |
nicklas |
877 |
<td><i>Data splitter</i></td> |
| 5788 |
06 Oct 11 |
nicklas |
878 |
<td>\t</td> |
| 5788 |
06 Oct 11 |
nicklas |
879 |
</tr> |
| 5788 |
06 Oct 11 |
nicklas |
880 |
<tr> |
| 5788 |
06 Oct 11 |
nicklas |
881 |
<td><i>Min data columns</i></td> |
| 5788 |
06 Oct 11 |
nicklas |
882 |
<td>4</td> |
| 5788 |
06 Oct 11 |
nicklas |
883 |
</tr> |
| 5788 |
06 Oct 11 |
nicklas |
884 |
<tr> |
| 5788 |
06 Oct 11 |
nicklas |
885 |
<td><i>Remove quotes</i></td> |
| 5788 |
06 Oct 11 |
nicklas |
886 |
<td>yes</td> |
| 5788 |
06 Oct 11 |
nicklas |
887 |
</tr> |
| 5788 |
06 Oct 11 |
nicklas |
888 |
<tr> |
| 5788 |
06 Oct 11 |
nicklas |
889 |
<td><i>Complex mappings</i></td> |
| 5788 |
06 Oct 11 |
nicklas |
890 |
<td>allow</td> |
| 5788 |
06 Oct 11 |
nicklas |
891 |
</tr> |
| 5788 |
06 Oct 11 |
nicklas |
892 |
<tr> |
| 5788 |
06 Oct 11 |
nicklas |
893 |
<td><i>Reporter ID</i></td> |
| 5788 |
06 Oct 11 |
nicklas |
894 |
<td>\<transcript_id>\@\<seqname>\</td> |
| 5788 |
06 Oct 11 |
nicklas |
895 |
</tr> |
| 5788 |
06 Oct 11 |
nicklas |
896 |
<tr> |
| 5788 |
06 Oct 11 |
nicklas |
897 |
<td><i>Feature ID</i></td> |
| 5788 |
06 Oct 11 |
nicklas |
898 |
<td>\<transcript_id>\@\<seqname>\</td> |
| 5788 |
06 Oct 11 |
nicklas |
899 |
</tr> |
| 5788 |
06 Oct 11 |
nicklas |
900 |
</table> |
| 5788 |
06 Oct 11 |
nicklas |
901 |
|
| 5788 |
06 Oct 11 |
nicklas |
902 |
</td> |
| 5788 |
06 Oct 11 |
nicklas |
903 |
</tr> |
| 5788 |
06 Oct 11 |
nicklas |
904 |
|
| 5788 |
06 Oct 11 |
nicklas |
905 |
<tr class="evenrow"> |
| 2568 |
22 Aug 06 |
nicklas |
906 |
<td>Raw data for project A</td> |
| 2568 |
22 Aug 06 |
nicklas |
907 |
<td>Raw data importer</td> |
| 2568 |
22 Aug 06 |
nicklas |
908 |
<td> |
| 2568 |
22 Aug 06 |
nicklas |
909 |
|
| 2568 |
22 Aug 06 |
nicklas |
910 |
<table border="0" cellspacing="0" cellpadding="2"> |
| 2568 |
22 Aug 06 |
nicklas |
911 |
<tr> |
| 5788 |
06 Oct 11 |
nicklas |
912 |
<td><b>File</b></td> |
| 5788 |
06 Oct 11 |
nicklas |
913 |
<td><code>mouse/<br>genepix.mouse.v4.37k.00h.gpr</code></td> |
| 5788 |
06 Oct 11 |
nicklas |
914 |
</tr> |
| 5788 |
06 Oct 11 |
nicklas |
915 |
<tr> |
| 2568 |
22 Aug 06 |
nicklas |
916 |
<td><i>Raw data type</i></td> |
| 2568 |
22 Aug 06 |
nicklas |
917 |
<td>Genepix</td> |
| 2568 |
22 Aug 06 |
nicklas |
918 |
</tr> |
| 2568 |
22 Aug 06 |
nicklas |
919 |
<tr> |
| 2568 |
22 Aug 06 |
nicklas |
920 |
<td><i>Header</i></td> |
| 2568 |
22 Aug 06 |
nicklas |
921 |
<td>"(.+)=(.*)"</td> |
| 2568 |
22 Aug 06 |
nicklas |
922 |
</tr> |
| 2568 |
22 Aug 06 |
nicklas |
923 |
<tr> |
| 2568 |
22 Aug 06 |
nicklas |
924 |
<td><i>Data header</i></td> |
| 2568 |
22 Aug 06 |
nicklas |
925 |
<td>"Block"\t"Column"\t"Row"\t"Name"\t"ID"\t.*"Ratio of Medians \(532\/635\)".*</td> |
| 2568 |
22 Aug 06 |
nicklas |
926 |
</tr> |
| 2568 |
22 Aug 06 |
nicklas |
927 |
<tr> |
| 2568 |
22 Aug 06 |
nicklas |
928 |
<td><i>Data splitter</i></td> |
| 2568 |
22 Aug 06 |
nicklas |
929 |
<td>\t</td> |
| 2568 |
22 Aug 06 |
nicklas |
930 |
</tr> |
| 2568 |
22 Aug 06 |
nicklas |
931 |
<tr> |
| 2568 |
22 Aug 06 |
nicklas |
932 |
<td><i>Min data columns</i></td> |
| 2568 |
22 Aug 06 |
nicklas |
933 |
<td>48</td> |
| 2568 |
22 Aug 06 |
nicklas |
934 |
</tr> |
| 2568 |
22 Aug 06 |
nicklas |
935 |
<tr> |
| 2568 |
22 Aug 06 |
nicklas |
936 |
<td><i>Max data columns</i></td> |
| 2568 |
22 Aug 06 |
nicklas |
937 |
<td>48</td> |
| 2568 |
22 Aug 06 |
nicklas |
938 |
</tr> |
| 2568 |
22 Aug 06 |
nicklas |
939 |
|
| 2568 |
22 Aug 06 |
nicklas |
940 |
<tr> |
| 2568 |
22 Aug 06 |
nicklas |
941 |
<td><i>Block</i></td> |
| 2568 |
22 Aug 06 |
nicklas |
942 |
<td>\Block\</td> |
| 2568 |
22 Aug 06 |
nicklas |
943 |
</tr> |
| 2568 |
22 Aug 06 |
nicklas |
944 |
<tr> |
| 2568 |
22 Aug 06 |
nicklas |
945 |
<td><i>Column</i></td> |
| 2568 |
22 Aug 06 |
nicklas |
946 |
<td>\Column\</td> |
| 2568 |
22 Aug 06 |
nicklas |
947 |
</tr> |
| 2568 |
22 Aug 06 |
nicklas |
948 |
<tr> |
| 2568 |
22 Aug 06 |
nicklas |
949 |
<td><i>Row</i></td> |
| 2568 |
22 Aug 06 |
nicklas |
950 |
<td>\Row\</td> |
| 2568 |
22 Aug 06 |
nicklas |
951 |
</tr> |
| 2568 |
22 Aug 06 |
nicklas |
952 |
<tr> |
| 2568 |
22 Aug 06 |
nicklas |
953 |
<td><i>X</i></td> |
| 2568 |
22 Aug 06 |
nicklas |
954 |
<td>\X\</td> |
| 2568 |
22 Aug 06 |
nicklas |
955 |
</tr> |
| 2568 |
22 Aug 06 |
nicklas |
956 |
<tr> |
| 2568 |
22 Aug 06 |
nicklas |
957 |
<td><i>Y</i></td> |
| 2568 |
22 Aug 06 |
nicklas |
958 |
<td>\Y\</td> |
| 2568 |
22 Aug 06 |
nicklas |
959 |
</tr> |
| 2568 |
22 Aug 06 |
nicklas |
960 |
<tr> |
| 2568 |
22 Aug 06 |
nicklas |
961 |
<td><i>Reporter ID</i></td> |
| 2568 |
22 Aug 06 |
nicklas |
962 |
<td>\ID\</td> |
| 2568 |
22 Aug 06 |
nicklas |
963 |
</tr> |
| 2568 |
22 Aug 06 |
nicklas |
964 |
<tr> |
| 2568 |
22 Aug 06 |
nicklas |
965 |
<td><i>Spot diameter</i></td> |
| 2568 |
22 Aug 06 |
nicklas |
966 |
<td>\Dia.\</td> |
| 2568 |
22 Aug 06 |
nicklas |
967 |
</tr> |
| 2568 |
22 Aug 06 |
nicklas |
968 |
<tr> |
| 2568 |
22 Aug 06 |
nicklas |
969 |
<td><i>Channel 1 foreground median</i></td> |
| 2568 |
22 Aug 06 |
nicklas |
970 |
<td>\F635 Median\</td> |
| 2568 |
22 Aug 06 |
nicklas |
971 |
</tr> |
| 2568 |
22 Aug 06 |
nicklas |
972 |
<tr> |
| 2568 |
22 Aug 06 |
nicklas |
973 |
<td><i>Channel 1 foreground mean</i></td> |
| 2568 |
22 Aug 06 |
nicklas |
974 |
<td>\F635 Mean\</td> |
| 2568 |
22 Aug 06 |
nicklas |
975 |
</tr> |
| 2568 |
22 Aug 06 |
nicklas |
976 |
<tr> |
| 2568 |
22 Aug 06 |
nicklas |
977 |
<td><i>Channel 1 foreground standard deviation</i></td> |
| 2568 |
22 Aug 06 |
nicklas |
978 |
<td>\F635 SD\</td> |
| 2568 |
22 Aug 06 |
nicklas |
979 |
</tr> |
| 2568 |
22 Aug 06 |
nicklas |
980 |
<tr> |
| 2568 |
22 Aug 06 |
nicklas |
981 |
<td><i>Channel 1 background median</i></td> |
| 2568 |
22 Aug 06 |
nicklas |
982 |
<td>\B635 Median\</td> |
| 2568 |
22 Aug 06 |
nicklas |
983 |
</tr> |
| 2568 |
22 Aug 06 |
nicklas |
984 |
<tr> |
| 2568 |
22 Aug 06 |
nicklas |
985 |
<td><i>Channel 1 background mean</i></td> |
| 2568 |
22 Aug 06 |
nicklas |
986 |
<td>\B635 Mean\</td> |
| 2568 |
22 Aug 06 |
nicklas |
987 |
</tr> |
| 2568 |
22 Aug 06 |
nicklas |
988 |
<tr> |
| 2568 |
22 Aug 06 |
nicklas |
989 |
<td><i>Channel 1 background standard deviation</i></td> |
| 2568 |
22 Aug 06 |
nicklas |
990 |
<td>\B635 SD\</td> |
| 2568 |
22 Aug 06 |
nicklas |
991 |
</tr> |
| 2568 |
22 Aug 06 |
nicklas |
992 |
<tr> |
| 2568 |
22 Aug 06 |
nicklas |
993 |
<td><i>Percent pixels within 1 standard deviation</i></td> |
| 2568 |
22 Aug 06 |
nicklas |
994 |
<td>\% > B635+1SD\</td> |
| 2568 |
22 Aug 06 |
nicklas |
995 |
</tr> |
| 2568 |
22 Aug 06 |
nicklas |
996 |
<tr> |
| 2568 |
22 Aug 06 |
nicklas |
997 |
<td><i>Percent pixels within 2 standard deviations</i></td> |
| 2568 |
22 Aug 06 |
nicklas |
998 |
<td>\% > B635+2SD\</td> |
| 2568 |
22 Aug 06 |
nicklas |
999 |
</tr> |
| 2568 |
22 Aug 06 |
nicklas |
1000 |
<tr> |
| 2568 |
22 Aug 06 |
nicklas |
1001 |
<td><i>Percent saturated pixels</i></td> |
| 2568 |
22 Aug 06 |
nicklas |
1002 |
<td>\F635 % Sat.\</td> |
| 2568 |
22 Aug 06 |
nicklas |
1003 |
</tr> |
| 2568 |
22 Aug 06 |
nicklas |
1004 |
<tr> |
| 2568 |
22 Aug 06 |
nicklas |
1005 |
<td><i>Channel 2 foreground median</i></td> |
| 2568 |
22 Aug 06 |
nicklas |
1006 |
<td>\F532 Median\</td> |
| 2568 |
22 Aug 06 |
nicklas |
1007 |
</tr> |
| 2568 |
22 Aug 06 |
nicklas |
1008 |
<tr> |
| 2568 |
22 Aug 06 |
nicklas |
1009 |
<td><i>Channel 2 foreground mean</i></td> |
| 2568 |
22 Aug 06 |
nicklas |
1010 |
<td>\F532 Mean\</td> |
| 2568 |
22 Aug 06 |
nicklas |
1011 |
</tr> |
| 2568 |
22 Aug 06 |
nicklas |
1012 |
<tr> |
| 2568 |
22 Aug 06 |
nicklas |
1013 |
<td><i>Channel 2 foreground standard deviation</i></td> |
| 2568 |
22 Aug 06 |
nicklas |
1014 |
<td>\F532 SD\</td> |
| 2568 |
22 Aug 06 |
nicklas |
1015 |
</tr> |
| 2568 |
22 Aug 06 |
nicklas |
1016 |
<tr> |
| 2568 |
22 Aug 06 |
nicklas |
1017 |
<td><i>Channel 2 background median</i></td> |
| 2568 |
22 Aug 06 |
nicklas |
1018 |
<td>\B532 Median\</td> |
| 2568 |
22 Aug 06 |
nicklas |
1019 |
</tr> |
| 2568 |
22 Aug 06 |
nicklas |
1020 |
<tr> |
| 2593 |
24 Aug 06 |
martin |
1021 |
<td><i>Channel 2 background mean</i></td> |
| 2593 |
24 Aug 06 |
martin |
1022 |
<td>\B532 Mean\</td> |
| 2593 |
24 Aug 06 |
martin |
1023 |
</tr> |
| 2593 |
24 Aug 06 |
martin |
1024 |
<tr> |
| 2568 |
22 Aug 06 |
nicklas |
1025 |
<td><i>Channel 2 background standard deviation</i></td> |
| 2568 |
22 Aug 06 |
nicklas |
1026 |
<td>\B532 SD\</td> |
| 2568 |
22 Aug 06 |
nicklas |
1027 |
</tr> |
| 2568 |
22 Aug 06 |
nicklas |
1028 |
<tr> |
| 2568 |
22 Aug 06 |
nicklas |
1029 |
<td><i>Percent pixels within 1 standard deviation</i></td> |
| 2568 |
22 Aug 06 |
nicklas |
1030 |
<td>\% > B532+1SD\</td> |
| 2568 |
22 Aug 06 |
nicklas |
1031 |
</tr> |
| 2568 |
22 Aug 06 |
nicklas |
1032 |
<tr> |
| 2568 |
22 Aug 06 |
nicklas |
1033 |
<td><i>Percent pixels within 2 standard deviations</i></td> |
| 2568 |
22 Aug 06 |
nicklas |
1034 |
<td>\% > B532+2SD\</td> |
| 2568 |
22 Aug 06 |
nicklas |
1035 |
</tr> |
| 2568 |
22 Aug 06 |
nicklas |
1036 |
<tr> |
| 2568 |
22 Aug 06 |
nicklas |
1037 |
<td><i>Percent saturated pixels</i></td> |
| 2568 |
22 Aug 06 |
nicklas |
1038 |
<td>\F532 % Sat.\</td> |
| 2568 |
22 Aug 06 |
nicklas |
1039 |
</tr> |
| 2568 |
22 Aug 06 |
nicklas |
1040 |
<tr> |
| 2568 |
22 Aug 06 |
nicklas |
1041 |
<td><i>Foreground pixels</i></td> |
| 2568 |
22 Aug 06 |
nicklas |
1042 |
<td>\F Pixels\</td> |
| 2568 |
22 Aug 06 |
nicklas |
1043 |
</tr> |
| 2568 |
22 Aug 06 |
nicklas |
1044 |
<tr> |
| 2568 |
22 Aug 06 |
nicklas |
1045 |
<td><i>Background pixels</i></td> |
| 2568 |
22 Aug 06 |
nicklas |
1046 |
<td>\B Pixels\</td> |
| 2568 |
22 Aug 06 |
nicklas |
1047 |
</tr> |
| 2568 |
22 Aug 06 |
nicklas |
1048 |
<tr> |
| 2568 |
22 Aug 06 |
nicklas |
1049 |
<td><i>Flags</i></td> |
| 2568 |
22 Aug 06 |
nicklas |
1050 |
<td>\Flags\</td> |
| 2568 |
22 Aug 06 |
nicklas |
1051 |
</tr> |
| 2568 |
22 Aug 06 |
nicklas |
1052 |
</table> |
| 2568 |
22 Aug 06 |
nicklas |
1053 |
|
| 2568 |
22 Aug 06 |
nicklas |
1054 |
</td> |
| 2568 |
22 Aug 06 |
nicklas |
1055 |
</tr> |
| 2568 |
22 Aug 06 |
nicklas |
1056 |
|
| 5788 |
06 Oct 11 |
nicklas |
1057 |
<tr class="oddrow"> |
| 2568 |
22 Aug 06 |
nicklas |
1058 |
<td>Raw data for project A (dye-swap)</td> |
| 2568 |
22 Aug 06 |
nicklas |
1059 |
<td>Raw data importer</td> |
| 2568 |
22 Aug 06 |
nicklas |
1060 |
<td> |
| 2751 |
20 Oct 06 |
nicklas |
1061 |
|
| 2568 |
22 Aug 06 |
nicklas |
1062 |
<table border="0" cellspacing="0" cellpadding="2"> |
| 2568 |
22 Aug 06 |
nicklas |
1063 |
<tr> |
| 5788 |
06 Oct 11 |
nicklas |
1064 |
<td><b>File</b></td> |
| 5788 |
06 Oct 11 |
nicklas |
1065 |
<td><code>mouse/<br>genepix.mouse.v4.37k.00h.dyeswap.gpr</code></td> |
| 5788 |
06 Oct 11 |
nicklas |
1066 |
</tr> |
| 5788 |
06 Oct 11 |
nicklas |
1067 |
<tr> |
| 2568 |
22 Aug 06 |
nicklas |
1068 |
<td><i>Raw data type</i></td> |
| 2568 |
22 Aug 06 |
nicklas |
1069 |
<td>Genepix</td> |
| 2568 |
22 Aug 06 |
nicklas |
1070 |
</tr> |
| 2568 |
22 Aug 06 |
nicklas |
1071 |
<tr> |
| 2568 |
22 Aug 06 |
nicklas |
1072 |
<td><i>Header</i></td> |
| 2568 |
22 Aug 06 |
nicklas |
1073 |
<td>"(.+)=(.*)"</td> |
| 2568 |
22 Aug 06 |
nicklas |
1074 |
</tr> |
| 2568 |
22 Aug 06 |
nicklas |
1075 |
<tr> |
| 2568 |
22 Aug 06 |
nicklas |
1076 |
<td><i>Data header</i></td> |
| 2568 |
22 Aug 06 |
nicklas |
1077 |
<td>"Block"\t"Column"\t"Row"\t"Name"\t"ID"\t.*"Ratio of Medians \(635\/532\)".*</td> |
| 2568 |
22 Aug 06 |
nicklas |
1078 |
</tr> |
| 2568 |
22 Aug 06 |
nicklas |
1079 |
<tr> |
| 2568 |
22 Aug 06 |
nicklas |
1080 |
<td><i>Data splitter</i></td> |
| 2568 |
22 Aug 06 |
nicklas |
1081 |
<td>\t</td> |
| 2568 |
22 Aug 06 |
nicklas |
1082 |
</tr> |
| 2568 |
22 Aug 06 |
nicklas |
1083 |
<tr> |
| 2568 |
22 Aug 06 |
nicklas |
1084 |
<td><i>Min data columns</i></td> |
| 2568 |
22 Aug 06 |
nicklas |
1085 |
<td>48</td> |
| 2568 |
22 Aug 06 |
nicklas |
1086 |
</tr> |
| 2568 |
22 Aug 06 |
nicklas |
1087 |
<tr> |
| 2568 |
22 Aug 06 |
nicklas |
1088 |
<td><i>Max data columns</i></td> |
| 2568 |
22 Aug 06 |
nicklas |
1089 |
<td>48</td> |
| 2568 |
22 Aug 06 |
nicklas |
1090 |
</tr> |
| 2568 |
22 Aug 06 |
nicklas |
1091 |
|
| 2568 |
22 Aug 06 |
nicklas |
1092 |
<tr> |
| 2568 |
22 Aug 06 |
nicklas |
1093 |
<td><i>Block</i></td> |
| 2568 |
22 Aug 06 |
nicklas |
1094 |
<td>\Block\</td> |
| 2568 |
22 Aug 06 |
nicklas |
1095 |
</tr> |
| 2568 |
22 Aug 06 |
nicklas |
1096 |
<tr> |
| 2568 |
22 Aug 06 |
nicklas |
1097 |
<td><i>Column</i></td> |
| 2568 |
22 Aug 06 |
nicklas |
1098 |
<td>\Column\</td> |
| 2568 |
22 Aug 06 |
nicklas |
1099 |
</tr> |
| 2568 |
22 Aug 06 |
nicklas |
1100 |
<tr> |
| 2568 |
22 Aug 06 |
nicklas |
1101 |
<td><i>Row</i></td> |
| 2568 |
22 Aug 06 |
nicklas |
1102 |
<td>\Row\</td> |
| 2568 |
22 Aug 06 |
nicklas |
1103 |
</tr> |
| 2568 |
22 Aug 06 |
nicklas |
1104 |
<tr> |
| 2568 |
22 Aug 06 |
nicklas |
1105 |
<td><i>X</i></td> |
| 2568 |
22 Aug 06 |
nicklas |
1106 |
<td>\X\</td> |
| 2568 |
22 Aug 06 |
nicklas |
1107 |
</tr> |
| 2568 |
22 Aug 06 |
nicklas |
1108 |
<tr> |
| 2568 |
22 Aug 06 |
nicklas |
1109 |
<td><i>Y</i></td> |
| 2568 |
22 Aug 06 |
nicklas |
1110 |
<td>\Y\</td> |
| 2568 |
22 Aug 06 |
nicklas |
1111 |
</tr> |
| 2568 |
22 Aug 06 |
nicklas |
1112 |
<tr> |
| 2568 |
22 Aug 06 |
nicklas |
1113 |
<td><i>Reporter ID</i></td> |
| 2568 |
22 Aug 06 |
nicklas |
1114 |
<td>\ID\</td> |
| 2568 |
22 Aug 06 |
nicklas |
1115 |
</tr> |
| 2568 |
22 Aug 06 |
nicklas |
1116 |
<tr> |
| 2568 |
22 Aug 06 |
nicklas |
1117 |
<td><i>Spot diameter</i></td> |
| 2568 |
22 Aug 06 |
nicklas |
1118 |
<td>\Dia.\</td> |
| 2568 |
22 Aug 06 |
nicklas |
1119 |
</tr> |
| 2568 |
22 Aug 06 |
nicklas |
1120 |
<tr> |
| 2568 |
22 Aug 06 |
nicklas |
1121 |
<td><i>Channel 1 foreground median</i></td> |
| 2568 |
22 Aug 06 |
nicklas |
1122 |
<td>\F532 Median\</td> |
| 2568 |
22 Aug 06 |
nicklas |
1123 |
</tr> |
| 2568 |
22 Aug 06 |
nicklas |
1124 |
<tr> |
| 2568 |
22 Aug 06 |
nicklas |
1125 |
<td><i>Channel 1 foreground mean</i></td> |
| 2568 |
22 Aug 06 |
nicklas |
1126 |
<td>\F532 Mean\</td> |
| 2568 |
22 Aug 06 |
nicklas |
1127 |
</tr> |
| 2568 |
22 Aug 06 |
nicklas |
1128 |
<tr> |
| 2568 |
22 Aug 06 |
nicklas |
1129 |
<td><i>Channel 1 foreground standard deviation</i></td> |
| 2568 |
22 Aug 06 |
nicklas |
1130 |
<td>\F532 SD\</td> |
| 2568 |
22 Aug 06 |
nicklas |
1131 |
</tr> |
| 2568 |
22 Aug 06 |
nicklas |
1132 |
<tr> |
| 2568 |
22 Aug 06 |
nicklas |
1133 |
<td><i>Channel 1 background median</i></td> |
| 2568 |
22 Aug 06 |
nicklas |
1134 |
<td>\B532 Median\</td> |
| 2568 |
22 Aug 06 |
nicklas |
1135 |
</tr> |
| 2568 |
22 Aug 06 |
nicklas |
1136 |
<tr> |
| 2568 |
22 Aug 06 |
nicklas |
1137 |
<td><i>Channel 1 background mean</i></td> |
| 2568 |
22 Aug 06 |
nicklas |
1138 |
<td>\B532 Mean\</td> |
| 2568 |
22 Aug 06 |
nicklas |
1139 |
</tr> |
| 2568 |
22 Aug 06 |
nicklas |
1140 |
<tr> |
| 2568 |
22 Aug 06 |
nicklas |
1141 |
<td><i>Channel 1 background standard deviation</i></td> |
| 2568 |
22 Aug 06 |
nicklas |
1142 |
<td>\B532 SD\</td> |
| 2568 |
22 Aug 06 |
nicklas |
1143 |
</tr> |
| 2568 |
22 Aug 06 |
nicklas |
1144 |
<tr> |
| 2568 |
22 Aug 06 |
nicklas |
1145 |
<td><i>Percent pixels within 1 standard deviation</i></td> |
| 2568 |
22 Aug 06 |
nicklas |
1146 |
<td>\% > B532+1SD\</td> |
| 2568 |
22 Aug 06 |
nicklas |
1147 |
</tr> |
| 2568 |
22 Aug 06 |
nicklas |
1148 |
<tr> |
| 2568 |
22 Aug 06 |
nicklas |
1149 |
<td><i>Percent pixels within 2 standard deviations</i></td> |
| 2568 |
22 Aug 06 |
nicklas |
1150 |
<td>\% > B532+2SD\</td> |
| 2568 |
22 Aug 06 |
nicklas |
1151 |
</tr> |
| 2568 |
22 Aug 06 |
nicklas |
1152 |
<tr> |
| 2568 |
22 Aug 06 |
nicklas |
1153 |
<td><i>Percent saturated pixels</i></td> |
| 2568 |
22 Aug 06 |
nicklas |
1154 |
<td>\F532 % Sat.\</td> |
| 2568 |
22 Aug 06 |
nicklas |
1155 |
</tr> |
| 2568 |
22 Aug 06 |
nicklas |
1156 |
<tr> |
| 2568 |
22 Aug 06 |
nicklas |
1157 |
<td><i>Channel 2 foreground median</i></td> |
| 2568 |
22 Aug 06 |
nicklas |
1158 |
<td>\F635 Median\</td> |
| 2568 |
22 Aug 06 |
nicklas |
1159 |
</tr> |
| 2568 |
22 Aug 06 |
nicklas |
1160 |
<tr> |
| 2568 |
22 Aug 06 |
nicklas |
1161 |
<td><i>Channel 2 foreground mean</i></td> |
| 2568 |
22 Aug 06 |
nicklas |
1162 |
<td>\F635 Mean\</td> |
| 2568 |
22 Aug 06 |
nicklas |
1163 |
</tr> |
| 2568 |
22 Aug 06 |
nicklas |
1164 |
<tr> |
| 2568 |
22 Aug 06 |
nicklas |
1165 |
<td><i>Channel 2 foreground standard deviation</i></td> |
| 2568 |
22 Aug 06 |
nicklas |
1166 |
<td>\F635 SD\</td> |
| 2568 |
22 Aug 06 |
nicklas |
1167 |
</tr> |
| 2568 |
22 Aug 06 |
nicklas |
1168 |
<tr> |
| 2568 |
22 Aug 06 |
nicklas |
1169 |
<td><i>Channel 2 background median</i></td> |
| 2568 |
22 Aug 06 |
nicklas |
1170 |
<td>\B635 Median\</td> |
| 2568 |
22 Aug 06 |
nicklas |
1171 |
</tr> |
| 2568 |
22 Aug 06 |
nicklas |
1172 |
<tr> |
| 2568 |
22 Aug 06 |
nicklas |
1173 |
<td><i>Channel 2 background mean</i></td> |
| 2568 |
22 Aug 06 |
nicklas |
1174 |
<td>\B635 Mean\</td> |
| 2568 |
22 Aug 06 |
nicklas |
1175 |
</tr> |
| 2568 |
22 Aug 06 |
nicklas |
1176 |
<tr> |
| 2568 |
22 Aug 06 |
nicklas |
1177 |
<td><i>Channel 2 background standard deviation</i></td> |
| 2568 |
22 Aug 06 |
nicklas |
1178 |
<td>\B635 SD\</td> |
| 2568 |
22 Aug 06 |
nicklas |
1179 |
</tr> |
| 2568 |
22 Aug 06 |
nicklas |
1180 |
<tr> |
| 2568 |
22 Aug 06 |
nicklas |
1181 |
<td><i>Percent pixels within 1 standard deviation</i></td> |
| 2568 |
22 Aug 06 |
nicklas |
1182 |
<td>\% > B635+1SD\</td> |
| 2568 |
22 Aug 06 |
nicklas |
1183 |
</tr> |
| 2568 |
22 Aug 06 |
nicklas |
1184 |
<tr> |
| 2568 |
22 Aug 06 |
nicklas |
1185 |
<td><i>Percent pixels within 2 standard deviations</i></td> |
| 2568 |
22 Aug 06 |
nicklas |
1186 |
<td>\% > B635+2SD\</td> |
| 2568 |
22 Aug 06 |
nicklas |
1187 |
</tr> |
| 2568 |
22 Aug 06 |
nicklas |
1188 |
<tr> |
| 2568 |
22 Aug 06 |
nicklas |
1189 |
<td><i>Percent saturated pixels</i></td> |
| 2568 |
22 Aug 06 |
nicklas |
1190 |
<td>\F635 % Sat.\</td> |
| 2568 |
22 Aug 06 |
nicklas |
1191 |
</tr> |
| 2568 |
22 Aug 06 |
nicklas |
1192 |
<tr> |
| 2568 |
22 Aug 06 |
nicklas |
1193 |
<td><i>Foreground pixels</i></td> |
| 2568 |
22 Aug 06 |
nicklas |
1194 |
<td>\F Pixels\</td> |
| 2568 |
22 Aug 06 |
nicklas |
1195 |
</tr> |
| 2568 |
22 Aug 06 |
nicklas |
1196 |
<tr> |
| 2568 |
22 Aug 06 |
nicklas |
1197 |
<td><i>Background pixels</i></td> |
| 2568 |
22 Aug 06 |
nicklas |
1198 |
<td>\B Pixels\</td> |
| 2568 |
22 Aug 06 |
nicklas |
1199 |
</tr> |
| 2568 |
22 Aug 06 |
nicklas |
1200 |
<tr> |
| 2568 |
22 Aug 06 |
nicklas |
1201 |
<td><i>Flags</i></td> |
| 2568 |
22 Aug 06 |
nicklas |
1202 |
<td>\Flags\</td> |
| 2568 |
22 Aug 06 |
nicklas |
1203 |
</tr> |
| 2568 |
22 Aug 06 |
nicklas |
1204 |
</table> |
| 2568 |
22 Aug 06 |
nicklas |
1205 |
|
| 2568 |
22 Aug 06 |
nicklas |
1206 |
</td> |
| 2568 |
22 Aug 06 |
nicklas |
1207 |
</tr> |
| 2568 |
22 Aug 06 |
nicklas |
1208 |
</table> |
| 2568 |
22 Aug 06 |
nicklas |
1209 |
<p> |
| 2568 |
22 Aug 06 |
nicklas |
1210 |
</li> |
| 2568 |
22 Aug 06 |
nicklas |
1211 |
|
| 2568 |
22 Aug 06 |
nicklas |
1212 |
<li> |
| 4025 |
30 Nov 07 |
nicklas |
1213 |
Annotate the file formats: |
| 4025 |
30 Nov 07 |
nicklas |
1214 |
<table class="listing" cellspacing="0" cellpadding="2" border="0"> |
| 4025 |
30 Nov 07 |
nicklas |
1215 |
<tr> |
| 4025 |
30 Nov 07 |
nicklas |
1216 |
<th>File format</th> |
| 4025 |
30 Nov 07 |
nicklas |
1217 |
<th>Annotation</th> |
| 4025 |
30 Nov 07 |
nicklas |
1218 |
<th>Value</th> |
| 4025 |
30 Nov 07 |
nicklas |
1219 |
</tr> |
| 4025 |
30 Nov 07 |
nicklas |
1220 |
<tr> |
| 4025 |
30 Nov 07 |
nicklas |
1221 |
<td>Raw data for project A</td> |
| 4025 |
30 Nov 07 |
nicklas |
1222 |
<td>Dye swap</td> |
| 4025 |
30 Nov 07 |
nicklas |
1223 |
<td>false</td> |
| 4025 |
30 Nov 07 |
nicklas |
1224 |
</tr> |
| 4025 |
30 Nov 07 |
nicklas |
1225 |
<tr> |
| 4025 |
30 Nov 07 |
nicklas |
1226 |
<td>Raw data for project A (dye swap)</td> |
| 4025 |
30 Nov 07 |
nicklas |
1227 |
<td>Dye swap</td> |
| 4025 |
30 Nov 07 |
nicklas |
1228 |
<td>true</td> |
| 4025 |
30 Nov 07 |
nicklas |
1229 |
</tr> |
| 4025 |
30 Nov 07 |
nicklas |
1230 |
</table> |
| 4025 |
30 Nov 07 |
nicklas |
1231 |
This will make the raw data importer automatically annotate the |
| 4025 |
30 Nov 07 |
nicklas |
1232 |
raw bioassays with the specified annotations. |
| 4025 |
30 Nov 07 |
nicklas |
1233 |
<p> |
| 4025 |
30 Nov 07 |
nicklas |
1234 |
</li> |
| 4025 |
30 Nov 07 |
nicklas |
1235 |
|
| 4025 |
30 Nov 07 |
nicklas |
1236 |
<li> |
| 2568 |
22 Aug 06 |
nicklas |
1237 |
Create plate type: |
| 2568 |
22 Aug 06 |
nicklas |
1238 |
<table class="listing" cellspacing="0" cellpadding="2" border="0"> |
| 2568 |
22 Aug 06 |
nicklas |
1239 |
<tr> |
| 2568 |
22 Aug 06 |
nicklas |
1240 |
<th>Name</th> |
| 2568 |
22 Aug 06 |
nicklas |
1241 |
<th>Geometry</th> |
| 2568 |
22 Aug 06 |
nicklas |
1242 |
</tr> |
| 2568 |
22 Aug 06 |
nicklas |
1243 |
<tr> |
| 2568 |
22 Aug 06 |
nicklas |
1244 |
<td>Plate type A</td> |
| 2568 |
22 Aug 06 |
nicklas |
1245 |
<td>384-well (16 x 24)</td> |
| 2568 |
22 Aug 06 |
nicklas |
1246 |
</tr> |
| 2568 |
22 Aug 06 |
nicklas |
1247 |
</table> |
| 2568 |
22 Aug 06 |
nicklas |
1248 |
<p> |
| 2568 |
22 Aug 06 |
nicklas |
1249 |
</li> |
| 2568 |
22 Aug 06 |
nicklas |
1250 |
|
| 2568 |
22 Aug 06 |
nicklas |
1251 |
<li> |
| 2568 |
22 Aug 06 |
nicklas |
1252 |
Import plates: |
| 2568 |
22 Aug 06 |
nicklas |
1253 |
<ol> |
| 2568 |
22 Aug 06 |
nicklas |
1254 |
<li>Go to the <code>Array LIMS -> Plates</code> page.</li> |
| 2568 |
22 Aug 06 |
nicklas |
1255 |
<li>Click on the <code>Import</code> button.</li> |
| 2568 |
22 Aug 06 |
nicklas |
1256 |
<li>Choose <code>auto-detect</code> and select |
| 2568 |
22 Aug 06 |
nicklas |
1257 |
the file <code>plates_and_reporters.mouse.v4.37k.txt</code>.</li> |
| 2568 |
22 Aug 06 |
nicklas |
1258 |
<li>The <code>Plates for project A</code> format should be |
| 2568 |
22 Aug 06 |
nicklas |
1259 |
found.</li> |
| 2568 |
22 Aug 06 |
nicklas |
1260 |
<li>Specify the following parameters: |
| 2568 |
22 Aug 06 |
nicklas |
1261 |
|
| 2568 |
22 Aug 06 |
nicklas |
1262 |
<table border="0" cellspacing="0" cellpadding="2"> |
| 2568 |
22 Aug 06 |
nicklas |
1263 |
<tr> |
| 2568 |
22 Aug 06 |
nicklas |
1264 |
<td><i>Plate type</i></td> |
| 2568 |
22 Aug 06 |
nicklas |
1265 |
<td>Plate type A</td> |
| 2568 |
22 Aug 06 |
nicklas |
1266 |
</tr> |
| 2568 |
22 Aug 06 |
nicklas |
1267 |
<tr> |
| 2568 |
22 Aug 06 |
nicklas |
1268 |
<td><i>Plate name prefix</i></td> |
| 2568 |
22 Aug 06 |
nicklas |
1269 |
<td>Plate A</td> |
| 2568 |
22 Aug 06 |
nicklas |
1270 |
</tr> |
| 2568 |
22 Aug 06 |
nicklas |
1271 |
<tr> |
| 2568 |
22 Aug 06 |
nicklas |
1272 |
<td><i>Plate name padding</i></td> |
| 2568 |
22 Aug 06 |
nicklas |
1273 |
<td>4</td> |
| 2568 |
22 Aug 06 |
nicklas |
1274 |
</tr> |
| 2568 |
22 Aug 06 |
nicklas |
1275 |
</table> |
| 2568 |
22 Aug 06 |
nicklas |
1276 |
</li> |
| 2568 |
22 Aug 06 |
nicklas |
1277 |
<li>Continue and wait for the import to finish. It should create 96 plates.</li> |
| 2568 |
22 Aug 06 |
nicklas |
1278 |
</ol> |
| 2568 |
22 Aug 06 |
nicklas |
1279 |
<p> |
| 2568 |
22 Aug 06 |
nicklas |
1280 |
</li> |
| 2568 |
22 Aug 06 |
nicklas |
1281 |
|
| 2568 |
22 Aug 06 |
nicklas |
1282 |
<li> |
| 5964 |
15 Feb 12 |
nicklas |
1283 |
Create array designs and upload data files to them. Keep the 'Set as project default' option checked |
| 5964 |
15 Feb 12 |
nicklas |
1284 |
if doing this manually. |
| 2568 |
22 Aug 06 |
nicklas |
1285 |
<table class="listing" cellspacing="0" cellpadding="2" border="0"> |
| 2568 |
22 Aug 06 |
nicklas |
1286 |
<tr> |
| 2568 |
22 Aug 06 |
nicklas |
1287 |
<th>Name</th> |
| 5788 |
06 Oct 11 |
nicklas |
1288 |
<th>Platform/Variant</th> |
| 3873 |
23 Oct 07 |
nicklas |
1289 |
<th>File(s)</th> |
| 2568 |
22 Aug 06 |
nicklas |
1290 |
</tr> |
| 2568 |
22 Aug 06 |
nicklas |
1291 |
<tr> |
| 2568 |
22 Aug 06 |
nicklas |
1292 |
<td>Array design A</td> |
| 3873 |
23 Oct 07 |
nicklas |
1293 |
<td>Generic</td> |
| 5788 |
06 Oct 11 |
nicklas |
1294 |
<td><i>Print map</i>: <code>mouse/printmap.mouse.v4.37k.tam</code></td> |
| 2568 |
22 Aug 06 |
nicklas |
1295 |
</tr> |
| 3873 |
23 Oct 07 |
nicklas |
1296 |
<tr> |
| 3873 |
23 Oct 07 |
nicklas |
1297 |
<td>Affymetrix A</td> |
| 3873 |
23 Oct 07 |
nicklas |
1298 |
<td>Affymetrix</td> |
| 5788 |
06 Oct 11 |
nicklas |
1299 |
<td><i>CDF file</i>: <code>affymtrix/cdf/MG_U74Av2.cdf</code></td> |
| 3873 |
23 Oct 07 |
nicklas |
1300 |
</tr> |
| 5788 |
06 Oct 11 |
nicklas |
1301 |
<tr> |
| 5788 |
06 Oct 11 |
nicklas |
1302 |
<td>RefSeqDesign A</td> |
| 5788 |
06 Oct 11 |
nicklas |
1303 |
<td>Sequencing/Expression-like</td> |
| 5788 |
06 Oct 11 |
nicklas |
1304 |
<td><i>GTF ref-seq file</i>: <code>sequencing/UCSC_Human_hg19_RefSeqGenes.gtf</code></td> |
| 5788 |
06 Oct 11 |
nicklas |
1305 |
</tr> |
| 2568 |
22 Aug 06 |
nicklas |
1306 |
</table> |
| 2568 |
22 Aug 06 |
nicklas |
1307 |
<p> |
| 4633 |
10 Nov 08 |
martin |
1308 |
Or |
| 4633 |
10 Nov 08 |
martin |
1309 |
<p> |
| 4633 |
10 Nov 08 |
martin |
1310 |
Import array designs with the ArrayDesignImporter plug-in. |
| 4633 |
10 Nov 08 |
martin |
1311 |
<ol> |
| 4633 |
10 Nov 08 |
martin |
1312 |
<li>Make sure the data-files, mentioned in table above, are located in <code>/home/power/</code>, upload them if not</li> |
| 4633 |
10 Nov 08 |
martin |
1313 |
<li>Click on the <code>Import</code> button on the array design list page.</li> |
| 4633 |
10 Nov 08 |
martin |
1314 |
<li>Choose ArrayDesignImporter in the plug-in drop-down list.</li> |
| 4633 |
10 Nov 08 |
martin |
1315 |
<li><b>Test with file:</b> <code>arraydesign_out.txt</code> and set |
| 4633 |
10 Nov 08 |
martin |
1316 |
the parsing parameters with help of the <code>Auto generate</code> button on the <code>Column mapping</code> |
| 4633 |
10 Nov 08 |
martin |
1317 |
tab.</li> |
| 4633 |
10 Nov 08 |
martin |
1318 |
<li>Start the import-job by clicking on the <code>Finish</code> button on the third wizard-page.</li> |
| 4633 |
10 Nov 08 |
martin |
1319 |
</ol> |
| 4633 |
10 Nov 08 |
martin |
1320 |
<p> |
| 2568 |
22 Aug 06 |
nicklas |
1321 |
</li> |
| 2568 |
22 Aug 06 |
nicklas |
1322 |
|
| 2568 |
22 Aug 06 |
nicklas |
1323 |
<li> |
| 3873 |
23 Oct 07 |
nicklas |
1324 |
Connect <code>Array design A</code> with plates. Select the imported plates (plate names starting |
| 3873 |
23 Oct 07 |
nicklas |
1325 |
with <code>Plate A</code>) and sort them in the correct order (as indicated by their names). |
| 2568 |
22 Aug 06 |
nicklas |
1326 |
<p> |
| 2568 |
22 Aug 06 |
nicklas |
1327 |
</li> |
| 2568 |
22 Aug 06 |
nicklas |
1328 |
|
| 2568 |
22 Aug 06 |
nicklas |
1329 |
<li> |
| 5788 |
06 Oct 11 |
nicklas |
1330 |
Import features to Array design A: |
| 2568 |
22 Aug 06 |
nicklas |
1331 |
<ol> |
| 2568 |
22 Aug 06 |
nicklas |
1332 |
<li>Click on the <code>Import</code> button when viewing properties for the array design.</li> |
| 5788 |
06 Oct 11 |
nicklas |
1333 |
<li>Choose <code>auto-detect</code> and use the file |
| 2568 |
22 Aug 06 |
nicklas |
1334 |
<code>printmap.mouse.v4.37k.tam</code>.</li> |
| 2682 |
02 Oct 06 |
jari |
1335 |
<li>The <code>Print map importer</code> plug-in should be |
| 2568 |
22 Aug 06 |
nicklas |
1336 |
found.</li> |
| 2568 |
22 Aug 06 |
nicklas |
1337 |
<li>Continue and wait for the import to finish. It should create 36,864 features and 48 blocks.</li> |
| 2568 |
22 Aug 06 |
nicklas |
1338 |
</ol> |
| 2568 |
22 Aug 06 |
nicklas |
1339 |
<p> |
| 5788 |
06 Oct 11 |
nicklas |
1340 |
Import features to RefSeqDesign A: |
| 5788 |
06 Oct 11 |
nicklas |
1341 |
<ol> |
| 5788 |
06 Oct 11 |
nicklas |
1342 |
<li>Click on the <code>Import</code> button when viewing properties for the array design.</li> |
| 5788 |
06 Oct 11 |
nicklas |
1343 |
<li>Choose <code>auto-detect</code> and use the file |
| 5788 |
06 Oct 11 |
nicklas |
1344 |
<code>UCSC_Human_hg19_RefSeqGenes.gtf</code>.</li> |
| 5788 |
06 Oct 11 |
nicklas |
1345 |
<li>The <code>GTF reporter map importer</code> plug-in should be |
| 5788 |
06 Oct 11 |
nicklas |
1346 |
found. Select the <code>GTF features for project A</code> format.</li> |
| 5788 |
06 Oct 11 |
nicklas |
1347 |
<li>Continue and wait for the import to finish. It should create 38,977 features and 1 block.</li> |
| 5788 |
06 Oct 11 |
nicklas |
1348 |
</ol> |
| 5788 |
06 Oct 11 |
nicklas |
1349 |
<p> |
| 2568 |
22 Aug 06 |
nicklas |
1350 |
</li> |
| 2568 |
22 Aug 06 |
nicklas |
1351 |
|
| 2568 |
22 Aug 06 |
nicklas |
1352 |
<li> |
| 4025 |
30 Nov 07 |
nicklas |
1353 |
Set project defaults. Go to the projects page and edit the |
| 4025 |
30 Nov 07 |
nicklas |
1354 |
<code>Project A</code> project. On the <code>Defaults</code> |
| 5964 |
15 Feb 12 |
nicklas |
1355 |
tab, set the following defaults. NOTE! Most of the items in this |
| 5964 |
15 Feb 12 |
nicklas |
1356 |
list should already be registered as default items if the |
| 6124 |
13 Sep 12 |
nicklas |
1357 |
'Add as project default' option was used when creating the new items. |
| 4025 |
30 Nov 07 |
nicklas |
1358 |
|
| 4025 |
30 Nov 07 |
nicklas |
1359 |
<table class="listing" cellspacing="0" cellpadding="2" border="0"> |
| 4025 |
30 Nov 07 |
nicklas |
1360 |
<tr> |
| 4025 |
30 Nov 07 |
nicklas |
1361 |
<th>Setting</th> |
| 5699 |
16 Aug 11 |
nicklas |
1362 |
<th>Value(s)</th> |
| 4025 |
30 Nov 07 |
nicklas |
1363 |
</tr> |
| 4025 |
30 Nov 07 |
nicklas |
1364 |
<tr> |
| 5699 |
16 Aug 11 |
nicklas |
1365 |
<td>Raw data type</td> |
| 5699 |
16 Aug 11 |
nicklas |
1366 |
<td>Genepix</td> |
| 4025 |
30 Nov 07 |
nicklas |
1367 |
</tr> |
| 4025 |
30 Nov 07 |
nicklas |
1368 |
<tr> |
| 5699 |
16 Aug 11 |
nicklas |
1369 |
<td>Platforms</td> |
| 5699 |
16 Aug 11 |
nicklas |
1370 |
<td> |
| 5699 |
16 Aug 11 |
nicklas |
1371 |
Generic<br> |
| 5699 |
16 Aug 11 |
nicklas |
1372 |
Affymetrix |
| 5699 |
16 Aug 11 |
nicklas |
1373 |
</td> |
| 4025 |
30 Nov 07 |
nicklas |
1374 |
</tr> |
| 4025 |
30 Nov 07 |
nicklas |
1375 |
<tr> |
| 5788 |
06 Oct 11 |
nicklas |
1376 |
<td>Platforms variants</td> |
| 5788 |
06 Oct 11 |
nicklas |
1377 |
<td> |
| 5788 |
06 Oct 11 |
nicklas |
1378 |
Sequencing / Expression-like |
| 5788 |
06 Oct 11 |
nicklas |
1379 |
</td> |
| 5788 |
06 Oct 11 |
nicklas |
1380 |
</tr> |
| 5788 |
06 Oct 11 |
nicklas |
1381 |
<tr> |
| 5699 |
16 Aug 11 |
nicklas |
1382 |
<td>Array designs</td> |
| 5699 |
16 Aug 11 |
nicklas |
1383 |
<td> |
| 5699 |
16 Aug 11 |
nicklas |
1384 |
Array design A<br> |
| 5788 |
06 Oct 11 |
nicklas |
1385 |
Affymetrix A<br> |
| 5788 |
06 Oct 11 |
nicklas |
1386 |
RefSeqDesign A |
| 5699 |
16 Aug 11 |
nicklas |
1387 |
</td> |
| 4025 |
30 Nov 07 |
nicklas |
1388 |
</tr> |
| 4025 |
30 Nov 07 |
nicklas |
1389 |
<tr> |
| 5699 |
16 Aug 11 |
nicklas |
1390 |
<td>Protocols</td> |
| 5699 |
16 Aug 11 |
nicklas |
1391 |
<td> |
| 5699 |
16 Aug 11 |
nicklas |
1392 |
Sampling A<br> |
| 5699 |
16 Aug 11 |
nicklas |
1393 |
Extraction A<br> |
| 5699 |
16 Aug 11 |
nicklas |
1394 |
Labeling A<br> |
| 5699 |
16 Aug 11 |
nicklas |
1395 |
Library preparation A<br> |
| 5699 |
16 Aug 11 |
nicklas |
1396 |
Hybridization A<br> |
| 5699 |
16 Aug 11 |
nicklas |
1397 |
cBot Settings A<br> |
| 5699 |
16 Aug 11 |
nicklas |
1398 |
Scanning A<br> |
| 5699 |
16 Aug 11 |
nicklas |
1399 |
HiSeq Settings A<br> |
| 5699 |
16 Aug 11 |
nicklas |
1400 |
TopHat Settings A<br> |
| 5699 |
16 Aug 11 |
nicklas |
1401 |
Feature extraction A<br> |
| 5699 |
16 Aug 11 |
nicklas |
1402 |
Cufflinks Settings A<br> |
| 5699 |
16 Aug 11 |
nicklas |
1403 |
Printing A |
| 5699 |
16 Aug 11 |
nicklas |
1404 |
</td> |
| 4025 |
30 Nov 07 |
nicklas |
1405 |
</tr> |
| 4025 |
30 Nov 07 |
nicklas |
1406 |
<tr> |
| 5699 |
16 Aug 11 |
nicklas |
1407 |
<td>Hardware</td> |
| 5699 |
16 Aug 11 |
nicklas |
1408 |
<td> |
| 5699 |
16 Aug 11 |
nicklas |
1409 |
Hybridization station A<br> |
| 5699 |
16 Aug 11 |
nicklas |
1410 |
cBot A<br> |
| 5699 |
16 Aug 11 |
nicklas |
1411 |
HiSeq 2000 A<br> |
| 5699 |
16 Aug 11 |
nicklas |
1412 |
Scanner A<br> |
| 5699 |
16 Aug 11 |
nicklas |
1413 |
Print robot A |
| 5699 |
16 Aug 11 |
nicklas |
1414 |
</td> |
| 4025 |
30 Nov 07 |
nicklas |
1415 |
</tr> |
| 4025 |
30 Nov 07 |
nicklas |
1416 |
<tr> |
| 5699 |
16 Aug 11 |
nicklas |
1417 |
<td>Software</td> |
| 5699 |
16 Aug 11 |
nicklas |
1418 |
<td> |
| 5699 |
16 Aug 11 |
nicklas |
1419 |
Software A<br> |
| 5699 |
16 Aug 11 |
nicklas |
1420 |
TopHat<br> |
| 5699 |
16 Aug 11 |
nicklas |
1421 |
Cufflinks |
| 5699 |
16 Aug 11 |
nicklas |
1422 |
</td> |
| 4025 |
30 Nov 07 |
nicklas |
1423 |
</tr> |
| 4025 |
30 Nov 07 |
nicklas |
1424 |
</table> |
| 4025 |
30 Nov 07 |
nicklas |
1425 |
|
| 4025 |
30 Nov 07 |
nicklas |
1426 |
<p> |
| 4025 |
30 Nov 07 |
nicklas |
1427 |
</li> |
| 4025 |
30 Nov 07 |
nicklas |
1428 |
|
| 4025 |
30 Nov 07 |
nicklas |
1429 |
<li> |
| 3873 |
23 Oct 07 |
nicklas |
1430 |
Create array batches: |
| 2568 |
22 Aug 06 |
nicklas |
1431 |
<table class="listing" cellspacing="0" cellpadding="2" border="0"> |
| 2568 |
22 Aug 06 |
nicklas |
1432 |
<tr> |
| 2568 |
22 Aug 06 |
nicklas |
1433 |
<th>Name</th> |
| 2568 |
22 Aug 06 |
nicklas |
1434 |
<th>Array design</th> |
| 2568 |
22 Aug 06 |
nicklas |
1435 |
<th>Print robot</th> |
| 2568 |
22 Aug 06 |
nicklas |
1436 |
<th>Protocol</th> |
| 2568 |
22 Aug 06 |
nicklas |
1437 |
</tr> |
| 2568 |
22 Aug 06 |
nicklas |
1438 |
<tr> |
| 2568 |
22 Aug 06 |
nicklas |
1439 |
<td>Array batch A</td> |
| 2568 |
22 Aug 06 |
nicklas |
1440 |
<td>Array design A</td> |
| 5788 |
06 Oct 11 |
nicklas |
1441 |
<td>Print robot A</td> |
| 2568 |
22 Aug 06 |
nicklas |
1442 |
<td>Printing A</td> |
| 2568 |
22 Aug 06 |
nicklas |
1443 |
</tr> |
| 3873 |
23 Oct 07 |
nicklas |
1444 |
<tr> |
| 3873 |
23 Oct 07 |
nicklas |
1445 |
<td>Affymetrix batch A</td> |
| 3873 |
23 Oct 07 |
nicklas |
1446 |
<td>Affymetrix A</td> |
| 3873 |
23 Oct 07 |
nicklas |
1447 |
<td></td> |
| 3873 |
23 Oct 07 |
nicklas |
1448 |
<td></td> |
| 3873 |
23 Oct 07 |
nicklas |
1449 |
</tr> |
| 2568 |
22 Aug 06 |
nicklas |
1450 |
</table> |
| 2568 |
22 Aug 06 |
nicklas |
1451 |
<p> |
| 4633 |
10 Nov 08 |
martin |
1452 |
Or |
| 4633 |
10 Nov 08 |
martin |
1453 |
<p> |
| 4633 |
10 Nov 08 |
martin |
1454 |
Import array batches with the ArrayBatchImporter plug-in. |
| 4633 |
10 Nov 08 |
martin |
1455 |
<ol> |
| 4633 |
10 Nov 08 |
martin |
1456 |
<li>Click on the <code>Import</code> button on the array batch list page.</li> |
| 4633 |
10 Nov 08 |
martin |
1457 |
<li>Select ArrayBatchImporter in the plug-in drop-down list and click <code>Next</code></li> |
| 4633 |
10 Nov 08 |
martin |
1458 |
<li><b>Test with file:</b> <code>arraybatch_out.txt</code> and set the parsing parameters |
| 4633 |
10 Nov 08 |
martin |
1459 |
with help of the <code>Auto generate</code> button on the <code>Column mapping</code> |
| 4633 |
10 Nov 08 |
martin |
1460 |
tab.</li> |
| 4633 |
10 Nov 08 |
martin |
1461 |
<li>Start the import-job by clicking on the <code>Finish</code> button on the third wizzard-page.</li> |
| 4633 |
10 Nov 08 |
martin |
1462 |
</ol> |
| 4633 |
10 Nov 08 |
martin |
1463 |
<p> |
| 2568 |
22 Aug 06 |
nicklas |
1464 |
</li> |
| 2568 |
22 Aug 06 |
nicklas |
1465 |
|
| 2568 |
22 Aug 06 |
nicklas |
1466 |
<li> |
| 2568 |
22 Aug 06 |
nicklas |
1467 |
Create array slides with the <code>Create slides</code> |
| 2568 |
22 Aug 06 |
nicklas |
1468 |
wizard. |
| 2568 |
22 Aug 06 |
nicklas |
1469 |
|
| 2568 |
22 Aug 06 |
nicklas |
1470 |
<table class="listing" cellspacing="0" cellpadding="2" border="0"> |
| 2568 |
22 Aug 06 |
nicklas |
1471 |
<tr> |
| 2568 |
22 Aug 06 |
nicklas |
1472 |
<th>Name</th> |
| 2568 |
22 Aug 06 |
nicklas |
1473 |
<th>Array batch</th> |
| 2568 |
22 Aug 06 |
nicklas |
1474 |
<th>Quantity</th> |
| 2568 |
22 Aug 06 |
nicklas |
1475 |
</tr> |
| 2568 |
22 Aug 06 |
nicklas |
1476 |
<tr> |
| 2568 |
22 Aug 06 |
nicklas |
1477 |
<td>Array slide A.</td> |
| 2568 |
22 Aug 06 |
nicklas |
1478 |
<td>Array batch A</td> |
| 2568 |
22 Aug 06 |
nicklas |
1479 |
<td>4</td> |
| 2568 |
22 Aug 06 |
nicklas |
1480 |
</tr> |
| 3873 |
23 Oct 07 |
nicklas |
1481 |
<tr> |
| 3873 |
23 Oct 07 |
nicklas |
1482 |
<td>Affymetrix slide A.</td> |
| 3873 |
23 Oct 07 |
nicklas |
1483 |
<td>Affymetrix batch A</td> |
| 3873 |
23 Oct 07 |
nicklas |
1484 |
<td>3</td> |
| 3873 |
23 Oct 07 |
nicklas |
1485 |
</tr> |
| 2568 |
22 Aug 06 |
nicklas |
1486 |
</table> |
| 2568 |
22 Aug 06 |
nicklas |
1487 |
<p> |
| 4633 |
10 Nov 08 |
martin |
1488 |
Or |
| 4633 |
10 Nov 08 |
martin |
1489 |
<p> |
| 4633 |
10 Nov 08 |
martin |
1490 |
Import array slides with the ArraySlideImporter plug-in. |
| 4633 |
10 Nov 08 |
martin |
1491 |
<ol> |
| 4633 |
10 Nov 08 |
martin |
1492 |
<li>Click on the <code>Import</code> button on the array slide list page.</li> |
| 4633 |
10 Nov 08 |
martin |
1493 |
<li>Select ArraySlideImporter in the plug-in drop-down list and click <code>Next</code></li> |
| 4633 |
10 Nov 08 |
martin |
1494 |
<li><b>Test with file:</b> <code>arrayslide_out.txt</code> and set the parsing parameters |
| 4633 |
10 Nov 08 |
martin |
1495 |
with help of the <code>Auto generate</code> button on the <code>Column mapping</code> |
| 4633 |
10 Nov 08 |
martin |
1496 |
tab.</li> |
| 4633 |
10 Nov 08 |
martin |
1497 |
<li>Start the import-job by clicking on the <code>Finish</code> button on the third wizzard-page.</li> |
| 4633 |
10 Nov 08 |
martin |
1498 |
</ol> |
| 4633 |
10 Nov 08 |
martin |
1499 |
<p> |
| 2568 |
22 Aug 06 |
nicklas |
1500 |
</li> |
| 2568 |
22 Aug 06 |
nicklas |
1501 |
</ol> |
| 2568 |
22 Aug 06 |
nicklas |
1502 |
|
| 2568 |
22 Aug 06 |
nicklas |
1503 |
<a name="user"></a> |
| 2568 |
22 Aug 06 |
nicklas |
1504 |
<h2>5. User tests</h2> |
| 2568 |
22 Aug 06 |
nicklas |
1505 |
<p> |
| 2568 |
22 Aug 06 |
nicklas |
1506 |
The user is a typical worker in the project. The user does the actual experimentation in the |
| 2568 |
22 Aug 06 |
nicklas |
1507 |
lab, which includes collecting samples, doing extraction, labeling and hybridizations. |
| 4633 |
10 Nov 08 |
martin |
1508 |
The user also scans and analyses the raw data resulting from the images. Inserting items can be |
| 4633 |
10 Nov 08 |
martin |
1509 |
done in two different ways, . |
| 2568 |
22 Aug 06 |
nicklas |
1510 |
</p> |
| 4789 |
24 Feb 09 |
nicklas |
1511 |
<h3>First step</h3> |
| 2568 |
22 Aug 06 |
nicklas |
1512 |
|
| 4789 |
24 Feb 09 |
nicklas |
1513 |
<ol> |
| 4789 |
24 Feb 09 |
nicklas |
1514 |
<li>Activate the <code>Project A</code> project. |
| 4789 |
24 Feb 09 |
nicklas |
1515 |
<p> |
| 5260 |
04 Mar 10 |
nicklas |
1516 |
|
| 2568 |
22 Aug 06 |
nicklas |
1517 |
<li> |
| 4789 |
24 Feb 09 |
nicklas |
1518 |
Create a bioplate: |
| 4789 |
24 Feb 09 |
nicklas |
1519 |
<table class="listing" cellspacing="0" cellpadding="2" border="0"> |
| 4789 |
24 Feb 09 |
nicklas |
1520 |
<tr> |
| 4789 |
24 Feb 09 |
nicklas |
1521 |
<th>Name</th> |
| 4789 |
24 Feb 09 |
nicklas |
1522 |
<th>Plate geometry</th> |
| 5260 |
04 Mar 10 |
nicklas |
1523 |
<th>Bioplate type</th> |
| 4789 |
24 Feb 09 |
nicklas |
1524 |
</tr> |
| 4789 |
24 Feb 09 |
nicklas |
1525 |
<tr> |
| 4789 |
24 Feb 09 |
nicklas |
1526 |
<td>Bioplate A</td> |
| 4789 |
24 Feb 09 |
nicklas |
1527 |
<td>96-well (8 x 12)</td> |
| 5260 |
04 Mar 10 |
nicklas |
1528 |
<td>BioPlate type A</td> |
| 4789 |
24 Feb 09 |
nicklas |
1529 |
</tr> |
| 4789 |
24 Feb 09 |
nicklas |
1530 |
</table> |
| 4789 |
24 Feb 09 |
nicklas |
1531 |
<p> |
| 4789 |
24 Feb 09 |
nicklas |
1532 |
<li>Continue with the second step, which can be done with batch importers or |
| 4789 |
24 Feb 09 |
nicklas |
1533 |
manually. |
| 4789 |
24 Feb 09 |
nicklas |
1534 |
|
| 4789 |
24 Feb 09 |
nicklas |
1535 |
</ol> |
| 4789 |
24 Feb 09 |
nicklas |
1536 |
|
| 4789 |
24 Feb 09 |
nicklas |
1537 |
|
| 4789 |
24 Feb 09 |
nicklas |
1538 |
<h3>Second step (using batch importers)</h3> |
| 4789 |
24 Feb 09 |
nicklas |
1539 |
|
| 4789 |
24 Feb 09 |
nicklas |
1540 |
<ol> |
| 4789 |
24 Feb 09 |
nicklas |
1541 |
<li>Click on the <code>Import</code> button on the list page.</li> |
| 4789 |
24 Feb 09 |
nicklas |
1542 |
<li>Select <itemtype>Importer in the plug-in drop-down list and click <code>Next</code></li> |
| 4789 |
24 Feb 09 |
nicklas |
1543 |
<li><b>Test with file:</b> using the right file(listed below) and set the parsing parameters |
| 4789 |
24 Feb 09 |
nicklas |
1544 |
by using the <code>Auto generate</code> button on the <code>Column mapping</code> tab. |
| 4789 |
24 Feb 09 |
nicklas |
1545 |
<table class="listing" cellspacing="0" cellpadding="2" border="0"> |
| 4789 |
24 Feb 09 |
nicklas |
1546 |
<tr> |
| 4789 |
24 Feb 09 |
nicklas |
1547 |
<th>Itemtype</th> |
| 4789 |
24 Feb 09 |
nicklas |
1548 |
<th>File</th> |
| 4789 |
24 Feb 09 |
nicklas |
1549 |
</tr> |
| 4789 |
24 Feb 09 |
nicklas |
1550 |
<tr> |
| 4789 |
24 Feb 09 |
nicklas |
1551 |
<td>Biosource</td> |
| 4789 |
24 Feb 09 |
nicklas |
1552 |
<td>biosource_out.txt</td> |
| 4789 |
24 Feb 09 |
nicklas |
1553 |
</tr> |
| 4789 |
24 Feb 09 |
nicklas |
1554 |
<tr> |
| 4789 |
24 Feb 09 |
nicklas |
1555 |
<td>Samples</td> |
| 4789 |
24 Feb 09 |
nicklas |
1556 |
<td>sample_out.txt</td> |
| 4789 |
24 Feb 09 |
nicklas |
1557 |
</tr> |
| 4789 |
24 Feb 09 |
nicklas |
1558 |
<tr> |
| 5700 |
17 Aug 11 |
nicklas |
1559 |
<td>Extracts (including labeled extracts and libraries)</td> |
| 4789 |
24 Feb 09 |
nicklas |
1560 |
<td>extract_out.txt</td> |
| 4789 |
24 Feb 09 |
nicklas |
1561 |
</tr> |
| 4789 |
24 Feb 09 |
nicklas |
1562 |
<tr> |
| 5700 |
17 Aug 11 |
nicklas |
1563 |
<td>Physical bioassays (hybridizations, flow cells)</td> |
| 5700 |
17 Aug 11 |
nicklas |
1564 |
<td>physicalbioassay_out.txt</td> |
| 4789 |
24 Feb 09 |
nicklas |
1565 |
</tr> |
| 4789 |
24 Feb 09 |
nicklas |
1566 |
<tr> |
| 5700 |
17 Aug 11 |
nicklas |
1567 |
<td>Derived bioassays (scans, assemblys)</td> |
| 5700 |
17 Aug 11 |
nicklas |
1568 |
<td>derivedbioassay_out.txt</td> |
| 4789 |
24 Feb 09 |
nicklas |
1569 |
</tr> |
| 4789 |
24 Feb 09 |
nicklas |
1570 |
<tr> |
| 4789 |
24 Feb 09 |
nicklas |
1571 |
<td>Raw bioassays</td> |
| 4789 |
24 Feb 09 |
nicklas |
1572 |
<td>rawbioassay_out.txt</td> |
| 4789 |
24 Feb 09 |
nicklas |
1573 |
</tr> |
| 4789 |
24 Feb 09 |
nicklas |
1574 |
</table> |
| 5983 |
23 Feb 12 |
nicklas |
1575 |
The files listed for biosource, samples, extracts, and derived bioassays also contain annotations |
| 4789 |
24 Feb 09 |
nicklas |
1576 |
for the items and these files should also be used with the annotation importer. |
| 4789 |
24 Feb 09 |
nicklas |
1577 |
The procedure is the same as for batch importers except that only <code>\Name\</code> |
| 4789 |
24 Feb 09 |
nicklas |
1578 |
is needed in the column mapping. The annotation column should be selected by default in |
| 5700 |
17 Aug 11 |
nicklas |
1579 |
the second wizard-step. |
| 4789 |
24 Feb 09 |
nicklas |
1580 |
</li> |
| 5700 |
17 Aug 11 |
nicklas |
1581 |
<li>Start the import-job by clicking on the <code>Finish</code> button on the third wizard-page.</li> |
| 4789 |
24 Feb 09 |
nicklas |
1582 |
<li>Continue with <a href="#step3">the third step</a>.</li> |
| 4789 |
24 Feb 09 |
nicklas |
1583 |
</ol> |
| 4789 |
24 Feb 09 |
nicklas |
1584 |
|
| 4789 |
24 Feb 09 |
nicklas |
1585 |
<h3>Second step (create items manually)</h3> |
| 4789 |
24 Feb 09 |
nicklas |
1586 |
<ol> |
| 4789 |
24 Feb 09 |
nicklas |
1587 |
<li> |
| 2568 |
22 Aug 06 |
nicklas |
1588 |
Create a biosource: |
| 2568 |
22 Aug 06 |
nicklas |
1589 |
<table class="listing" cellspacing="0" cellpadding="2" border="0"> |
| 2568 |
22 Aug 06 |
nicklas |
1590 |
<tr> |
| 2568 |
22 Aug 06 |
nicklas |
1591 |
<th>Name</th> |
| 2568 |
22 Aug 06 |
nicklas |
1592 |
<th>Annotations</th> |
| 2568 |
22 Aug 06 |
nicklas |
1593 |
</tr> |
| 2568 |
22 Aug 06 |
nicklas |
1594 |
<tr> |
| 2568 |
22 Aug 06 |
nicklas |
1595 |
<td>Biosource A</td> |
| 2568 |
22 Aug 06 |
nicklas |
1596 |
<td> |
| 2568 |
22 Aug 06 |
nicklas |
1597 |
<table border="0" cellspacing="0" cellpadding="2"> |
| 2568 |
22 Aug 06 |
nicklas |
1598 |
<tr> |
| 2568 |
22 Aug 06 |
nicklas |
1599 |
<td><i>Drug resistance:</i></td> |
| 2568 |
22 Aug 06 |
nicklas |
1600 |
<td>medium</td> |
| 2568 |
22 Aug 06 |
nicklas |
1601 |
</tr> |
| 2568 |
22 Aug 06 |
nicklas |
1602 |
</table> |
| 2568 |
22 Aug 06 |
nicklas |
1603 |
</td> |
| 2568 |
22 Aug 06 |
nicklas |
1604 |
</tr> |
| 2568 |
22 Aug 06 |
nicklas |
1605 |
</table> |
| 2568 |
22 Aug 06 |
nicklas |
1606 |
<p> |
| 2568 |
22 Aug 06 |
nicklas |
1607 |
</li> |
| 2568 |
22 Aug 06 |
nicklas |
1608 |
|
| 2568 |
22 Aug 06 |
nicklas |
1609 |
<li> |
| 2568 |
22 Aug 06 |
nicklas |
1610 |
Create samples: |
| 2568 |
22 Aug 06 |
nicklas |
1611 |
<table class="listing" cellspacing="0" cellpadding="2" border="0"> |
| 2568 |
22 Aug 06 |
nicklas |
1612 |
<tr> |
| 2568 |
22 Aug 06 |
nicklas |
1613 |
<th>Name</th> |
| 2568 |
22 Aug 06 |
nicklas |
1614 |
<th>Protocol</th> |
| 2568 |
22 Aug 06 |
nicklas |
1615 |
<th>Biosource</th> |
| 4789 |
24 Feb 09 |
nicklas |
1616 |
<th>Bioplate [well]</th> |
| 2568 |
22 Aug 06 |
nicklas |
1617 |
<th>Annotations</th> |
| 2568 |
22 Aug 06 |
nicklas |
1618 |
</tr> |
| 2568 |
22 Aug 06 |
nicklas |
1619 |
<tr> |
| 2568 |
22 Aug 06 |
nicklas |
1620 |
<td>Sample A.00h</td> |
| 2568 |
22 Aug 06 |
nicklas |
1621 |
<td>Sampling A</td> |
| 2568 |
22 Aug 06 |
nicklas |
1622 |
<td>Biosource A</td> |
| 5091 |
31 Aug 09 |
nicklas |
1623 |
<td>Bioplate A [A1]</td> |
| 2568 |
22 Aug 06 |
nicklas |
1624 |
<td> |
| 2568 |
22 Aug 06 |
nicklas |
1625 |
<table border="0" cellspacing="0" cellpadding="2"> |
| 2568 |
22 Aug 06 |
nicklas |
1626 |
<tr> |
| 4669 |
26 Nov 08 |
nicklas |
1627 |
<td><i>Time:</i></td> |
| 4669 |
26 Nov 08 |
nicklas |
1628 |
<td>0h</td> |
| 2568 |
22 Aug 06 |
nicklas |
1629 |
</tr> |
| 2568 |
22 Aug 06 |
nicklas |
1630 |
</table> |
| 2568 |
22 Aug 06 |
nicklas |
1631 |
</td> |
| 2568 |
22 Aug 06 |
nicklas |
1632 |
</tr> |
| 2568 |
22 Aug 06 |
nicklas |
1633 |
<tr> |
| 2568 |
22 Aug 06 |
nicklas |
1634 |
<td>Sample A.24h</td> |
| 2568 |
22 Aug 06 |
nicklas |
1635 |
<td>Sampling A</td> |
| 2568 |
22 Aug 06 |
nicklas |
1636 |
<td>Biosource A</td> |
| 5091 |
31 Aug 09 |
nicklas |
1637 |
<td>Bioplate A [A2]</td> |
| 2568 |
22 Aug 06 |
nicklas |
1638 |
<td> |
| 2568 |
22 Aug 06 |
nicklas |
1639 |
<table border="0" cellspacing="0" cellpadding="2"> |
| 2568 |
22 Aug 06 |
nicklas |
1640 |
<tr> |
| 4669 |
26 Nov 08 |
nicklas |
1641 |
<td><i>Time:</i></td> |
| 4669 |
26 Nov 08 |
nicklas |
1642 |
<td>24h</td> |
| 2568 |
22 Aug 06 |
nicklas |
1643 |
</tr> |
| 2568 |
22 Aug 06 |
nicklas |
1644 |
</table> |
| 2568 |
22 Aug 06 |
nicklas |
1645 |
</td> |
| 2568 |
22 Aug 06 |
nicklas |
1646 |
</tr> |
| 2568 |
22 Aug 06 |
nicklas |
1647 |
<tr> |
| 2568 |
22 Aug 06 |
nicklas |
1648 |
<td>Sample A.ref</td> |
| 2568 |
22 Aug 06 |
nicklas |
1649 |
<td>Sampling A</td> |
| 2568 |
22 Aug 06 |
nicklas |
1650 |
<td>-</td> |
| 5091 |
31 Aug 09 |
nicklas |
1651 |
<td>Bioplate A [A3]</td> |
| 2568 |
22 Aug 06 |
nicklas |
1652 |
<td>-</td> |
| 2568 |
22 Aug 06 |
nicklas |
1653 |
</tr> |
| 2568 |
22 Aug 06 |
nicklas |
1654 |
</table> |
| 2568 |
22 Aug 06 |
nicklas |
1655 |
<p> |
| 2568 |
22 Aug 06 |
nicklas |
1656 |
</li> |
| 2568 |
22 Aug 06 |
nicklas |
1657 |
|
| 2568 |
22 Aug 06 |
nicklas |
1658 |
<li> |
| 2568 |
22 Aug 06 |
nicklas |
1659 |
Create extracts: |
| 2568 |
22 Aug 06 |
nicklas |
1660 |
<table class="listing" cellspacing="0" cellpadding="2" border="0"> |
| 2568 |
22 Aug 06 |
nicklas |
1661 |
<tr> |
| 2568 |
22 Aug 06 |
nicklas |
1662 |
<th>Name</th> |
| 6021 |
19 Mar 12 |
nicklas |
1663 |
<th>Type</th> |
| 2568 |
22 Aug 06 |
nicklas |
1664 |
<th>Protocol</th> |
| 5983 |
23 Feb 12 |
nicklas |
1665 |
<th>Parent</th> |
| 4789 |
24 Feb 09 |
nicklas |
1666 |
<th>Bioplate [well]</th> |
| 5983 |
23 Feb 12 |
nicklas |
1667 |
<th>Annotations</th> |
| 2568 |
22 Aug 06 |
nicklas |
1668 |
</tr> |
| 2568 |
22 Aug 06 |
nicklas |
1669 |
<tr> |
| 2568 |
22 Aug 06 |
nicklas |
1670 |
<td>Extract A.00h</td> |
| 6021 |
19 Mar 12 |
nicklas |
1671 |
<td>-</td> |
| 2568 |
22 Aug 06 |
nicklas |
1672 |
<td>Extraction A</td> |
| 2568 |
22 Aug 06 |
nicklas |
1673 |
<td>Sample A.00h</td> |
| 5091 |
31 Aug 09 |
nicklas |
1674 |
<td>Bioplate A [B1]</td> |
| 5983 |
23 Feb 12 |
nicklas |
1675 |
<td>-</td> |
| 2568 |
22 Aug 06 |
nicklas |
1676 |
</tr> |
| 2568 |
22 Aug 06 |
nicklas |
1677 |
<tr> |
| 2568 |
22 Aug 06 |
nicklas |
1678 |
<td>Extract A.24h</td> |
| 6021 |
19 Mar 12 |
nicklas |
1679 |
<td>-</td> |
| 2568 |
22 Aug 06 |
nicklas |
1680 |
<td>Extraction A</td> |
| 2568 |
22 Aug 06 |
nicklas |
1681 |
<td>Sample A.24h</td> |
| 5091 |
31 Aug 09 |
nicklas |
1682 |
<td>Bioplate A [B2]</td> |
| 5983 |
23 Feb 12 |
nicklas |
1683 |
<td>-</td> |
| 2568 |
22 Aug 06 |
nicklas |
1684 |
</tr> |
| 2568 |
22 Aug 06 |
nicklas |
1685 |
<tr> |
| 2568 |
22 Aug 06 |
nicklas |
1686 |
<td>Extract A.ref</td> |
| 6021 |
19 Mar 12 |
nicklas |
1687 |
<td>-</td> |
| 2568 |
22 Aug 06 |
nicklas |
1688 |
<td>Extraction A</td> |
| 2568 |
22 Aug 06 |
nicklas |
1689 |
<td>Sample A.ref</td> |
| 5091 |
31 Aug 09 |
nicklas |
1690 |
<td>Bioplate A [B3]</td> |
| 5983 |
23 Feb 12 |
nicklas |
1691 |
<td>-</td> |
| 2568 |
22 Aug 06 |
nicklas |
1692 |
</tr> |
| 5983 |
23 Feb 12 |
nicklas |
1693 |
<tr> |
| 5983 |
23 Feb 12 |
nicklas |
1694 |
<td>Extract A.00h.qc</td> |
| 6021 |
19 Mar 12 |
nicklas |
1695 |
<td>Quality control</td> |
| 5983 |
23 Feb 12 |
nicklas |
1696 |
<td>-</td> |
| 5983 |
23 Feb 12 |
nicklas |
1697 |
<td>Extract A.00h</td> |
| 5983 |
23 Feb 12 |
nicklas |
1698 |
<td>-</td> |
| 5983 |
23 Feb 12 |
nicklas |
1699 |
<td> |
| 5983 |
23 Feb 12 |
nicklas |
1700 |
<table border="0" cellspacing="0" cellpadding="2"> |
| 5983 |
23 Feb 12 |
nicklas |
1701 |
<tr> |
| 5983 |
23 Feb 12 |
nicklas |
1702 |
<td><i>RIN:</i></td> |
| 5983 |
23 Feb 12 |
nicklas |
1703 |
<td>8.1</td> |
| 5983 |
23 Feb 12 |
nicklas |
1704 |
</tr> |
| 5983 |
23 Feb 12 |
nicklas |
1705 |
</table> |
| 5983 |
23 Feb 12 |
nicklas |
1706 |
</td> |
| 5983 |
23 Feb 12 |
nicklas |
1707 |
</tr> |
| 5983 |
23 Feb 12 |
nicklas |
1708 |
<tr> |
| 5983 |
23 Feb 12 |
nicklas |
1709 |
<td>Extract A.24h.qc</td> |
| 6021 |
19 Mar 12 |
nicklas |
1710 |
<td>Quality control</td> |
| 5983 |
23 Feb 12 |
nicklas |
1711 |
<td>-</td> |
| 5983 |
23 Feb 12 |
nicklas |
1712 |
<td>Extract A.24h</td> |
| 5983 |
23 Feb 12 |
nicklas |
1713 |
<td>-</td> |
| 5983 |
23 Feb 12 |
nicklas |
1714 |
<td> |
| 5983 |
23 Feb 12 |
nicklas |
1715 |
<table border="0" cellspacing="0" cellpadding="2"> |
| 5983 |
23 Feb 12 |
nicklas |
1716 |
<tr> |
| 5983 |
23 Feb 12 |
nicklas |
1717 |
<td><i>RIN:</i></td> |
| 5983 |
23 Feb 12 |
nicklas |
1718 |
<td>8.5</td> |
| 5983 |
23 Feb 12 |
nicklas |
1719 |
</tr> |
| 5983 |
23 Feb 12 |
nicklas |
1720 |
</table> |
| 5983 |
23 Feb 12 |
nicklas |
1721 |
</td> |
| 5983 |
23 Feb 12 |
nicklas |
1722 |
</tr> |
| 5983 |
23 Feb 12 |
nicklas |
1723 |
<tr> |
| 5983 |
23 Feb 12 |
nicklas |
1724 |
<td>Extract A.ref.qc</td> |
| 6021 |
19 Mar 12 |
nicklas |
1725 |
<td>Quality control</td> |
| 5983 |
23 Feb 12 |
nicklas |
1726 |
<td>-</td> |
| 5983 |
23 Feb 12 |
nicklas |
1727 |
<td>Extract A.ref</td> |
| 5983 |
23 Feb 12 |
nicklas |
1728 |
<td>-</td> |
| 5983 |
23 Feb 12 |
nicklas |
1729 |
<td> |
| 5983 |
23 Feb 12 |
nicklas |
1730 |
<table border="0" cellspacing="0" cellpadding="2"> |
| 5983 |
23 Feb 12 |
nicklas |
1731 |
<tr> |
| 5983 |
23 Feb 12 |
nicklas |
1732 |
<td><i>RIN:</i></td> |
| 5983 |
23 Feb 12 |
nicklas |
1733 |
<td>9.2</td> |
| 5983 |
23 Feb 12 |
nicklas |
1734 |
</tr> |
| 5983 |
23 Feb 12 |
nicklas |
1735 |
</table> |
| 5983 |
23 Feb 12 |
nicklas |
1736 |
</td> |
| 5983 |
23 Feb 12 |
nicklas |
1737 |
</tr> |
| 2568 |
22 Aug 06 |
nicklas |
1738 |
</table> |
| 2568 |
22 Aug 06 |
nicklas |
1739 |
<p> |
| 2568 |
22 Aug 06 |
nicklas |
1740 |
</li> |
| 2568 |
22 Aug 06 |
nicklas |
1741 |
|
| 2568 |
22 Aug 06 |
nicklas |
1742 |
<li> |
| 5699 |
16 Aug 11 |
nicklas |
1743 |
Create labeled extracts and libraries: |
| 2568 |
22 Aug 06 |
nicklas |
1744 |
<table class="listing" cellspacing="0" cellpadding="2" border="0"> |
| 2568 |
22 Aug 06 |
nicklas |
1745 |
<tr> |
| 2568 |
22 Aug 06 |
nicklas |
1746 |
<th>Name</th> |
| 5788 |
06 Oct 11 |
nicklas |
1747 |
<th>Type</th> |
| 2568 |
22 Aug 06 |
nicklas |
1748 |
<th>Label</th> |
| 2568 |
22 Aug 06 |
nicklas |
1749 |
<th>Protocol</th> |
| 2568 |
22 Aug 06 |
nicklas |
1750 |
<th>Extract</th> |
| 4789 |
24 Feb 09 |
nicklas |
1751 |
<th>Bioplate [well]</th> |
| 2568 |
22 Aug 06 |
nicklas |
1752 |
</tr> |
| 2568 |
22 Aug 06 |
nicklas |
1753 |
<tr> |
| 2568 |
22 Aug 06 |
nicklas |
1754 |
<td>Labeled extract A.00h</td> |
| 5788 |
06 Oct 11 |
nicklas |
1755 |
<td>Labeled extract</td> |
| 2568 |
22 Aug 06 |
nicklas |
1756 |
<td>cy3</td> |
| 2568 |
22 Aug 06 |
nicklas |
1757 |
<td>Labeling A</td> |
| 2568 |
22 Aug 06 |
nicklas |
1758 |
<td>Extract A.00h</td> |
| 5091 |
31 Aug 09 |
nicklas |
1759 |
<td>Bioplate A [C1]</td> |
| 2568 |
22 Aug 06 |
nicklas |
1760 |
</tr> |
| 2568 |
22 Aug 06 |
nicklas |
1761 |
<tr> |
| 2568 |
22 Aug 06 |
nicklas |
1762 |
<td>Labeled extract A.24h</td> |
| 5788 |
06 Oct 11 |
nicklas |
1763 |
<td>Labeled extract</td> |
| 2568 |
22 Aug 06 |
nicklas |
1764 |
<td>cy3</td> |
| 2568 |
22 Aug 06 |
nicklas |
1765 |
<td>Labeling A</td> |
| 2568 |
22 Aug 06 |
nicklas |
1766 |
<td>Extract A.24h</td> |
| 5091 |
31 Aug 09 |
nicklas |
1767 |
<td>Bioplate A [C2]</td> |
| 2568 |
22 Aug 06 |
nicklas |
1768 |
</tr> |
| 2568 |
22 Aug 06 |
nicklas |
1769 |
<tr> |
| 2568 |
22 Aug 06 |
nicklas |
1770 |
<td>Labeled extract A.ref</td> |
| 5788 |
06 Oct 11 |
nicklas |
1771 |
<td>Labeled extract</td> |
| 2568 |
22 Aug 06 |
nicklas |
1772 |
<td>cy5</td> |
| 2568 |
22 Aug 06 |
nicklas |
1773 |
<td>Labeling A</td> |
| 2568 |
22 Aug 06 |
nicklas |
1774 |
<td>Extract A.ref</td> |
| 5091 |
31 Aug 09 |
nicklas |
1775 |
<td>Bioplate A [C3]</td> |
| 2568 |
22 Aug 06 |
nicklas |
1776 |
</tr> |
| 2568 |
22 Aug 06 |
nicklas |
1777 |
<tr class="shaded"> |
| 2568 |
22 Aug 06 |
nicklas |
1778 |
<td>Labeled extract A.00h (dye-swap)</td> |
| 5788 |
06 Oct 11 |
nicklas |
1779 |
<td>Labeled extract</td> |
| 2568 |
22 Aug 06 |
nicklas |
1780 |
<td>cy5</td> |
| 2568 |
22 Aug 06 |
nicklas |
1781 |
<td>Labeling A</td> |
| 2568 |
22 Aug 06 |
nicklas |
1782 |
<td>Extract A.00h</td> |
| 5091 |
31 Aug 09 |
nicklas |
1783 |
<td>Bioplate A [D1]</td> |
| 2568 |
22 Aug 06 |
nicklas |
1784 |
</tr> |
| 2568 |
22 Aug 06 |
nicklas |
1785 |
<tr class="shaded"> |
| 2568 |
22 Aug 06 |
nicklas |
1786 |
<td>Labeled extract A.24h (dye-swap)</td> |
| 5788 |
06 Oct 11 |
nicklas |
1787 |
<td>Labeled extract</td> |
| 2568 |
22 Aug 06 |
nicklas |
1788 |
<td>cy5</td> |
| 2568 |
22 Aug 06 |
nicklas |
1789 |
<td>Labeling A</td> |
| 2568 |
22 Aug 06 |
nicklas |
1790 |
<td>Extract A.24h</td> |
| 5091 |
31 Aug 09 |
nicklas |
1791 |
<td>Bioplate A [D2]</td> |
| 2568 |
22 Aug 06 |
nicklas |
1792 |
</tr> |
| 2568 |
22 Aug 06 |
nicklas |
1793 |
<tr class="shaded"> |
| 2568 |
22 Aug 06 |
nicklas |
1794 |
<td>Labeled extract A.ref (dye-swap)</td> |
| 5788 |
06 Oct 11 |
nicklas |
1795 |
<td>Labeled extract</td> |
| 2568 |
22 Aug 06 |
nicklas |
1796 |
<td>cy3</td> |
| 2568 |
22 Aug 06 |
nicklas |
1797 |
<td>Labeling A</td> |
| 2568 |
22 Aug 06 |
nicklas |
1798 |
<td>Extract A.ref</td> |
| 5091 |
31 Aug 09 |
nicklas |
1799 |
<td>Bioplate A [D3]</td> |
| 2568 |
22 Aug 06 |
nicklas |
1800 |
</tr> |
| 5699 |
16 Aug 11 |
nicklas |
1801 |
<tr> |
| 5699 |
16 Aug 11 |
nicklas |
1802 |
<td>Library A.00h</td> |
| 5788 |
06 Oct 11 |
nicklas |
1803 |
<td>Library</td> |
| 5699 |
16 Aug 11 |
nicklas |
1804 |
<td>-</td> |
| 5699 |
16 Aug 11 |
nicklas |
1805 |
<td>Library preparation A</td> |
| 5699 |
16 Aug 11 |
nicklas |
1806 |
<td>Extract A.00h</td> |
| 5699 |
16 Aug 11 |
nicklas |
1807 |
<td>Bioplate A [E1]</td> |
| 5699 |
16 Aug 11 |
nicklas |
1808 |
</tr> |
| 5699 |
16 Aug 11 |
nicklas |
1809 |
<tr> |
| 5699 |
16 Aug 11 |
nicklas |
1810 |
<td>Library A.24h</td> |
| 5788 |
06 Oct 11 |
nicklas |
1811 |
<td>Library</td> |
| 5699 |
16 Aug 11 |
nicklas |
1812 |
<td>-</td> |
| 5699 |
16 Aug 11 |
nicklas |
1813 |
<td>Library preparation A</td> |
| 5699 |
16 Aug 11 |
nicklas |
1814 |
<td>Extract A.24h</td> |
| 5699 |
16 Aug 11 |
nicklas |
1815 |
<td>Bioplate A [E2]</td> |
| 5699 |
16 Aug 11 |
nicklas |
1816 |
</tr> |
| 2568 |
22 Aug 06 |
nicklas |
1817 |
</table> |
| 2568 |
22 Aug 06 |
nicklas |
1818 |
<p> |
| 2568 |
22 Aug 06 |
nicklas |
1819 |
</li> |
| 2568 |
22 Aug 06 |
nicklas |
1820 |
|
| 2568 |
22 Aug 06 |
nicklas |
1821 |
<li> |
| 5699 |
16 Aug 11 |
nicklas |
1822 |
Create physical bioassays (hybridizations and flow cells): |
| 2568 |
22 Aug 06 |
nicklas |
1823 |
<table class="listing" cellspacing="0" cellpadding="2" border="0"> |
| 2568 |
22 Aug 06 |
nicklas |
1824 |
<tr> |
| 2568 |
22 Aug 06 |
nicklas |
1825 |
<th>Name</th> |
| 2568 |
22 Aug 06 |
nicklas |
1826 |
<th>Protocol</th> |
| 2568 |
22 Aug 06 |
nicklas |
1827 |
<th>Hardware</th> |
| 2568 |
22 Aug 06 |
nicklas |
1828 |
<th>Array slide</th> |
| 5699 |
16 Aug 11 |
nicklas |
1829 |
<th>Extracts (position)</th> |
| 2568 |
22 Aug 06 |
nicklas |
1830 |
</tr> |
| 2568 |
22 Aug 06 |
nicklas |
1831 |
<tr> |
| 2568 |
22 Aug 06 |
nicklas |
1832 |
<td>Hybridization A.00h</td> |
| 2568 |
22 Aug 06 |
nicklas |
1833 |
<td>Hybridization A</td> |
| 2568 |
22 Aug 06 |
nicklas |
1834 |
<td>Hybridization station A</td> |
| 2568 |
22 Aug 06 |
nicklas |
1835 |
<td>Array slide A.1</td> |
| 2568 |
22 Aug 06 |
nicklas |
1836 |
<td>Labeled extract A.00h,<br>Labeled extract A.ref</td> |
| 2568 |
22 Aug 06 |
nicklas |
1837 |
</tr> |
| 2568 |
22 Aug 06 |
nicklas |
1838 |
<tr> |
| 2568 |
22 Aug 06 |
nicklas |
1839 |
<td>Hybridization A.24h</td> |
| 2568 |
22 Aug 06 |
nicklas |
1840 |
<td>Hybridization A</td> |
| 2568 |
22 Aug 06 |
nicklas |
1841 |
<td>Hybridization station A</td> |
| 2568 |
22 Aug 06 |
nicklas |
1842 |
<td>Array slide A.2</td> |
| 2568 |
22 Aug 06 |
nicklas |
1843 |
<td>Labeled extract A.24h,<br>Labeled extract A.ref</td> |
| 2568 |
22 Aug 06 |
nicklas |
1844 |
</tr> |
| 2568 |
22 Aug 06 |
nicklas |
1845 |
<tr class="shaded"> |
| 2568 |
22 Aug 06 |
nicklas |
1846 |
<td>Hybridization A.00h (dye-swap)</td> |
| 2568 |
22 Aug 06 |
nicklas |
1847 |
<td>Hybridization A</td> |
| 2568 |
22 Aug 06 |
nicklas |
1848 |
<td>Hybridization station A</td> |
| 2568 |
22 Aug 06 |
nicklas |
1849 |
<td>Array slide A.3</td> |
| 2568 |
22 Aug 06 |
nicklas |
1850 |
<td>Labeled extract A.00h (dye-swap),<br>Labeled extract A.ref (dye-swap)</td> |
| 2568 |
22 Aug 06 |
nicklas |
1851 |
</tr> |
| 2568 |
22 Aug 06 |
nicklas |
1852 |
<tr class="shaded"> |
| 2568 |
22 Aug 06 |
nicklas |
1853 |
<td>Hybridization A.24h (dye-swap)</td> |
| 2568 |
22 Aug 06 |
nicklas |
1854 |
<td>Hybridization A</td> |
| 2568 |
22 Aug 06 |
nicklas |
1855 |
<td>Hybridization station A</td> |
| 2568 |
22 Aug 06 |
nicklas |
1856 |
<td>Array slide A.4</td> |
| 2568 |
22 Aug 06 |
nicklas |
1857 |
<td>Labeled extract A.24h (dye-swap),<br>Labeled extract A.ref (dye-swap)</td> |
| 2568 |
22 Aug 06 |
nicklas |
1858 |
</tr> |
| 3873 |
23 Oct 07 |
nicklas |
1859 |
<tr> |
| 3873 |
23 Oct 07 |
nicklas |
1860 |
<td>Affymetrix hyb A.1</td> |
| 3873 |
23 Oct 07 |
nicklas |
1861 |
<td>Hybridization A</td> |
| 3873 |
23 Oct 07 |
nicklas |
1862 |
<td>Hybridization station A</td> |
| 3873 |
23 Oct 07 |
nicklas |
1863 |
<td>Affymetrix slide A.1</td> |
| 3873 |
23 Oct 07 |
nicklas |
1864 |
<td>Labeled extract A.00h</td> |
| 3873 |
23 Oct 07 |
nicklas |
1865 |
</tr> |
| 3873 |
23 Oct 07 |
nicklas |
1866 |
<tr> |
| 3873 |
23 Oct 07 |
nicklas |
1867 |
<td>Affymetrix hyb A.2</td> |
| 3873 |
23 Oct 07 |
nicklas |
1868 |
<td>Hybridization A</td> |
| 3873 |
23 Oct 07 |
nicklas |
1869 |
<td>Hybridization station A</td> |
| 3873 |
23 Oct 07 |
nicklas |
1870 |
<td>Affymetrix slide A.2</td> |
| 3873 |
23 Oct 07 |
nicklas |
1871 |
<td>Labeled extract A.24h</td> |
| 3873 |
23 Oct 07 |
nicklas |
1872 |
</tr> |
| 3873 |
23 Oct 07 |
nicklas |
1873 |
<tr> |
| 3873 |
23 Oct 07 |
nicklas |
1874 |
<td>Affymetrix hyb A.3</td> |
| 3873 |
23 Oct 07 |
nicklas |
1875 |
<td>Hybridization A</td> |
| 3873 |
23 Oct 07 |
nicklas |
1876 |
<td>Hybridization station A</td> |
| 3873 |
23 Oct 07 |
nicklas |
1877 |
<td>Affymetrix slide A.3</td> |
| 3873 |
23 Oct 07 |
nicklas |
1878 |
<td>Labeled extract A.ref</td> |
| 3873 |
23 Oct 07 |
nicklas |
1879 |
</tr> |
| 5699 |
16 Aug 11 |
nicklas |
1880 |
<tr class="shaded"> |
| 5699 |
16 Aug 11 |
nicklas |
1881 |
<td>Flow cell A</td> |
| 5699 |
16 Aug 11 |
nicklas |
1882 |
<td>cBot Settings A</td> |
| 5699 |
16 Aug 11 |
nicklas |
1883 |
<td>cBot A</td> |
| 5699 |
16 Aug 11 |
nicklas |
1884 |
<td>-</td> |
| 6124 |
13 Sep 12 |
nicklas |
1885 |
<td>Library A.00h (1),<br>Library A.24h (2)</td> |
| 5699 |
16 Aug 11 |
nicklas |
1886 |
</tr> |
| 2568 |
22 Aug 06 |
nicklas |
1887 |
</table> |
| 2568 |
22 Aug 06 |
nicklas |
1888 |
<p> |
| 2568 |
22 Aug 06 |
nicklas |
1889 |
</li> |
| 2568 |
22 Aug 06 |
nicklas |
1890 |
|
| 2568 |
22 Aug 06 |
nicklas |
1891 |
<li> |
| 5788 |
06 Oct 11 |
nicklas |
1892 |
Create derived bioassays (scans, arrangements, etc.): |
| 2568 |
22 Aug 06 |
nicklas |
1893 |
<table class="listing" cellspacing="0" cellpadding="2" border="0"> |
| 2568 |
22 Aug 06 |
nicklas |
1894 |
<tr> |
| 2568 |
22 Aug 06 |
nicklas |
1895 |
<th>Name</th> |
| 5699 |
16 Aug 11 |
nicklas |
1896 |
<th>Parent bioasasay</th> |
| 5699 |
16 Aug 11 |
nicklas |
1897 |
<th>Parent extract</th> |
| 5699 |
16 Aug 11 |
nicklas |
1898 |
<th>Hardware/Software</th> |
| 2568 |
22 Aug 06 |
nicklas |
1899 |
<th>Protocol</th> |
| 5144 |
20 Oct 09 |
nicklas |
1900 |
<th>PMT gain</th> |
| 2568 |
22 Aug 06 |
nicklas |
1901 |
</tr> |
| 2568 |
22 Aug 06 |
nicklas |
1902 |
<tr> |
| 2568 |
22 Aug 06 |
nicklas |
1903 |
<td>Scan A.00h</td> |
| 2568 |
22 Aug 06 |
nicklas |
1904 |
<td>Hybridization A.00h</td> |
| 5788 |
06 Oct 11 |
nicklas |
1905 |
<td>-</td> |
| 5699 |
16 Aug 11 |
nicklas |
1906 |
<td>HW: Scanner A</td> |
| 2568 |
22 Aug 06 |
nicklas |
1907 |
<td>Scanning A</td> |
| 5144 |
20 Oct 09 |
nicklas |
1908 |
<td>400 V</td> |
| 2568 |
22 Aug 06 |
nicklas |
1909 |
</tr> |
| 2568 |
22 Aug 06 |
nicklas |
1910 |
<tr> |
| 2568 |
22 Aug 06 |
nicklas |
1911 |
<td>Scan A.24h</td> |
| 2568 |
22 Aug 06 |
nicklas |
1912 |
<td>Hybridization A.24h</td> |
| 5788 |
06 Oct 11 |
nicklas |
1913 |
<td>-</td> |
| 5699 |
16 Aug 11 |
nicklas |
1914 |
<td>HW: Scanner A</td> |
| 2568 |
22 Aug 06 |
nicklas |
1915 |
<td>Scanning A</td> |
| 5144 |
20 Oct 09 |
nicklas |
1916 |
<td>500 V</td> |
| 2568 |
22 Aug 06 |
nicklas |
1917 |
</tr> |
| 2568 |
22 Aug 06 |
nicklas |
1918 |
<tr class="shaded"> |
| 2568 |
22 Aug 06 |
nicklas |
1919 |
<td>Scan A.00h (dye-swap)</td> |
| 2568 |
22 Aug 06 |
nicklas |
1920 |
<td>Hybridization A.00h (dye-swap)</td> |
| 5788 |
06 Oct 11 |
nicklas |
1921 |
<td>-</td> |
| 5699 |
16 Aug 11 |
nicklas |
1922 |
<td>HW: Scanner A</td> |
| 2568 |
22 Aug 06 |
nicklas |
1923 |
<td>Scanning A</td> |
| 5144 |
20 Oct 09 |
nicklas |
1924 |
<td>600 V</td> |
| 2568 |
22 Aug 06 |
nicklas |
1925 |
</tr> |
| 2568 |
22 Aug 06 |
nicklas |
1926 |
<tr class="shaded"> |
| 2568 |
22 Aug 06 |
nicklas |
1927 |
<td>Scan A.24h (dye-swap)</td> |
| 2568 |
22 Aug 06 |
nicklas |
1928 |
<td>Hybridization A.24h (dye-swap)</td> |
| 5788 |
06 Oct 11 |
nicklas |
1929 |
<td>-</td> |
| 5699 |
16 Aug 11 |
nicklas |
1930 |
<td>HW: Scanner A</td> |
| 2568 |
22 Aug 06 |
nicklas |
1931 |
<td>Scanning A</td> |
| 5144 |
20 Oct 09 |
nicklas |
1932 |
<td>700 V</td> |
| 2568 |
22 Aug 06 |
nicklas |
1933 |
</tr> |
| 3873 |
23 Oct 07 |
nicklas |
1934 |
<tr> |
| 3873 |
23 Oct 07 |
nicklas |
1935 |
<td>Affymetrix scan A.1</td> |
| 3873 |
23 Oct 07 |
nicklas |
1936 |
<td>Affymetrix hyb A.1</td> |
| 5788 |
06 Oct 11 |
nicklas |
1937 |
<td>-</td> |
| 5699 |
16 Aug 11 |
nicklas |
1938 |
<td>HW: Scanner A</td> |
| 3873 |
23 Oct 07 |
nicklas |
1939 |
<td>Scanning A</td> |
| 5144 |
20 Oct 09 |
nicklas |
1940 |
<td>800 V</td> |
| 3873 |
23 Oct 07 |
nicklas |
1941 |
</tr> |
| 3873 |
23 Oct 07 |
nicklas |
1942 |
<tr> |
| 3873 |
23 Oct 07 |
nicklas |
1943 |
<td>Affymetrix scan A.2</td> |
| 3873 |
23 Oct 07 |
nicklas |
1944 |
<td>Affymetrix hyb A.2</td> |
| 5788 |
06 Oct 11 |
nicklas |
1945 |
<td>-</td> |
| 5699 |
16 Aug 11 |
nicklas |
1946 |
<td>HW: Scanner A</td> |
| 3873 |
23 Oct 07 |
nicklas |
1947 |
<td>Scanning A</td> |
| 5144 |
20 Oct 09 |
nicklas |
1948 |
<td>900 V</td> |
| 3873 |
23 Oct 07 |
nicklas |
1949 |
</tr> |
| 3873 |
23 Oct 07 |
nicklas |
1950 |
<tr> |
| 3873 |
23 Oct 07 |
nicklas |
1951 |
<td>Affymetrix scan A.3</td> |
| 3873 |
23 Oct 07 |
nicklas |
1952 |
<td>Affymetrix hyb A.3</td> |
| 5788 |
06 Oct 11 |
nicklas |
1953 |
<td>-</td> |
| 5699 |
16 Aug 11 |
nicklas |
1954 |
<td>HW: Scanner A</td> |
| 3873 |
23 Oct 07 |
nicklas |
1955 |
<td>Scanning A</td> |
| 5144 |
20 Oct 09 |
nicklas |
1956 |
<td>1000 V</td> |
| 3873 |
23 Oct 07 |
nicklas |
1957 |
</tr> |
| 5699 |
16 Aug 11 |
nicklas |
1958 |
<tr class="shaded"> |
| 5699 |
16 Aug 11 |
nicklas |
1959 |
<td>Sequenced A</td> |
| 5699 |
16 Aug 11 |
nicklas |
1960 |
<td>Flow cell A</td> |
| 5699 |
16 Aug 11 |
nicklas |
1961 |
<td>-</td> |
| 5699 |
16 Aug 11 |
nicklas |
1962 |
<td>HW: HiSeq 2000 A</td> |
| 5699 |
16 Aug 11 |
nicklas |
1963 |
<td>HiSeq Settings A</td> |
| 5699 |
16 Aug 11 |
nicklas |
1964 |
<td>-</td> |
| 5699 |
16 Aug 11 |
nicklas |
1965 |
</tr> |
| 5699 |
16 Aug 11 |
nicklas |
1966 |
<tr class="shaded"> |
| 5788 |
06 Oct 11 |
nicklas |
1967 |
<td>Arrangement A.00h</td> |
| 5699 |
16 Aug 11 |
nicklas |
1968 |
<td>Sequenced A</td> |
| 5699 |
16 Aug 11 |
nicklas |
1969 |
<td>Library A.00h</td> |
| 5699 |
16 Aug 11 |
nicklas |
1970 |
<td>SW: TopHat</td> |
| 5699 |
16 Aug 11 |
nicklas |
1971 |
<td>TopHat Settings A</td> |
| 5699 |
16 Aug 11 |
nicklas |
1972 |
<td>-</td> |
| 5699 |
16 Aug 11 |
nicklas |
1973 |
</tr> |
| 5699 |
16 Aug 11 |
nicklas |
1974 |
<tr class="shaded"> |
| 5788 |
06 Oct 11 |
nicklas |
1975 |
<td>Arrangement A.24h</td> |
| 5699 |
16 Aug 11 |
nicklas |
1976 |
<td>Sequenced A</td> |
| 5699 |
16 Aug 11 |
nicklas |
1977 |
<td>Library A.24h</td> |
| 5699 |
16 Aug 11 |
nicklas |
1978 |
<td>SW: TopHat</td> |
| 5699 |
16 Aug 11 |
nicklas |
1979 |
<td>TopHat Settings A</td> |
| 5699 |
16 Aug 11 |
nicklas |
1980 |
<td>-</td> |
| 5699 |
16 Aug 11 |
nicklas |
1981 |
</tr> |
| 2568 |
22 Aug 06 |
nicklas |
1982 |
</table> |
| 2568 |
22 Aug 06 |
nicklas |
1983 |
<p> |
| 2568 |
22 Aug 06 |
nicklas |
1984 |
</li> |
| 2568 |
22 Aug 06 |
nicklas |
1985 |
|
| 2568 |
22 Aug 06 |
nicklas |
1986 |
<li> |
| 2568 |
22 Aug 06 |
nicklas |
1987 |
Create raw bioassays: |
| 2568 |
22 Aug 06 |
nicklas |
1988 |
<table class="listing" cellspacing="0" cellpadding="2" border="0"> |
| 2568 |
22 Aug 06 |
nicklas |
1989 |
<tr> |
| 2568 |
22 Aug 06 |
nicklas |
1990 |
<th>Name</th> |
| 3873 |
23 Oct 07 |
nicklas |
1991 |
<th>Platform/Raw data type</th> |
| 5699 |
16 Aug 11 |
nicklas |
1992 |
<th>Parent bioassay</th> |
| 5699 |
16 Aug 11 |
nicklas |
1993 |
<th>Parent extract</th> |
| 2568 |
22 Aug 06 |
nicklas |
1994 |
<th>Array design</th> |
| 2568 |
22 Aug 06 |
nicklas |
1995 |
<th>Protocol</th> |
| 2568 |
22 Aug 06 |
nicklas |
1996 |
<th>Software</th> |
| 3873 |
23 Oct 07 |
nicklas |
1997 |
<th>File(s)</th> |
| 2568 |
22 Aug 06 |
nicklas |
1998 |
</tr> |
| 2568 |
22 Aug 06 |
nicklas |
1999 |
<tr> |
| 2568 |
22 Aug 06 |
nicklas |
2000 |
<td>Raw bioassay A.00h</td> |
| 3873 |
23 Oct 07 |
nicklas |
2001 |
<td>Generic/GenePix</td> |
| 5699 |
16 Aug 11 |
nicklas |
2002 |
<td>Scan A.00h</td> |
| 5788 |
06 Oct 11 |
nicklas |
2003 |
<td>-</td> |
| 2568 |
22 Aug 06 |
nicklas |
2004 |
<td>Array design A</td> |
| 2568 |
22 Aug 06 |
nicklas |
2005 |
<td>Feature extraction A</td> |
| 2568 |
22 Aug 06 |
nicklas |
2006 |
<td>Software A</td> |
| 5788 |
06 Oct 11 |
nicklas |
2007 |
<td><i>Raw data</i>: <code>mouse/genepix.mouse.v4.37k.00h.gpr</code></td> |
| 2568 |
22 Aug 06 |
nicklas |
2008 |
</tr> |
| 2568 |
22 Aug 06 |
nicklas |
2009 |
<tr> |
| 2568 |
22 Aug 06 |
nicklas |
2010 |
<td>Raw bioassay A.24h</td> |
| 3873 |
23 Oct 07 |
nicklas |
2011 |
<td>Generic/GenePix</td> |
| 5699 |
16 Aug 11 |
nicklas |
2012 |
<td>Scan A.24h</td> |
| 5788 |
06 Oct 11 |
nicklas |
2013 |
<td>-</td> |
| 2568 |
22 Aug 06 |
nicklas |
2014 |
<td>Array design A</td> |
| 2568 |
22 Aug 06 |
nicklas |
2015 |
<td>Feature extraction A</td> |
| 2568 |
22 Aug 06 |
nicklas |
2016 |
<td>Software A</td> |
| 5788 |
06 Oct 11 |
nicklas |
2017 |
<td><i>Raw data</i>: <code>mouse/genepix.mouse.v4.37k.24h.gpr</code></td> |
| 2568 |
22 Aug 06 |
nicklas |
2018 |
</tr> |
| 2568 |
22 Aug 06 |
nicklas |
2019 |
<tr class="shaded"> |
| 2568 |
22 Aug 06 |
nicklas |
2020 |
<td>Raw bioassay A.00h (dye-swap)</td> |
| 3873 |
23 Oct 07 |
nicklas |
2021 |
<td>Generic/GenePix</td> |
| 5699 |
16 Aug 11 |
nicklas |
2022 |
<td>Scan A.00h (dye-swap)</td> |
| 5788 |
06 Oct 11 |
nicklas |
2023 |
<td>-</td> |
| 2568 |
22 Aug 06 |
nicklas |
2024 |
<td>Array design A</td> |
| 2568 |
22 Aug 06 |
nicklas |
2025 |
<td>Feature extraction A</td> |
| 2568 |
22 Aug 06 |
nicklas |
2026 |
<td>Software A</td> |
| 5788 |
06 Oct 11 |
nicklas |
2027 |
<td><i>Raw data</i>: <code>mouse/genepix.mouse.v4.37k.00h.dyeswap.gpr</code></td> |
| 2568 |
22 Aug 06 |
nicklas |
2028 |
</tr> |
| 2568 |
22 Aug 06 |
nicklas |
2029 |
<tr class="shaded"> |
| 2568 |
22 Aug 06 |
nicklas |
2030 |
<td>Raw bioassay A.24h (dye-swap)</td> |
| 3873 |
23 Oct 07 |
nicklas |
2031 |
<td>Generic/GenePix</td> |
| 5699 |
16 Aug 11 |
nicklas |
2032 |
<td>Scan A.24h (dye-swap)</td> |
| 5788 |
06 Oct 11 |
nicklas |
2033 |
<td>-</td> |
| 2568 |
22 Aug 06 |
nicklas |
2034 |
<td>Array design A</td> |
| 2568 |
22 Aug 06 |
nicklas |
2035 |
<td>Feature extraction A</td> |
| 2568 |
22 Aug 06 |
nicklas |
2036 |
<td>Software A</td> |
| 5788 |
06 Oct 11 |
nicklas |
2037 |
<td><i>Raw data</i>: <code>mouse/genepix.mouse.v4.37k.24h.dyeswap.gpr</code></td> |
| 2568 |
22 Aug 06 |
nicklas |
2038 |
</tr> |
| 3873 |
23 Oct 07 |
nicklas |
2039 |
<tr> |
| 3873 |
23 Oct 07 |
nicklas |
2040 |
<td>Affymetrix raw A.1</td> |
| 3873 |
23 Oct 07 |
nicklas |
2041 |
<td>Affymetrix</td> |
| 5699 |
16 Aug 11 |
nicklas |
2042 |
<td>Affymetrix scan A.1</td> |
| 5788 |
06 Oct 11 |
nicklas |
2043 |
<td>-</td> |
| 3873 |
23 Oct 07 |
nicklas |
2044 |
<td>Affymetrix A</td> |
| 3873 |
23 Oct 07 |
nicklas |
2045 |
<td>Feature extraction A</td> |
| 3873 |
23 Oct 07 |
nicklas |
2046 |
<td>Software A</td> |
| 5788 |
06 Oct 11 |
nicklas |
2047 |
<td><i>CEL file</i>: <code>affymetrix/E-TEST-1.ebi.ac.uk/jos1761.cel</code></td> |
| 3873 |
23 Oct 07 |
nicklas |
2048 |
</tr> |
| 3873 |
23 Oct 07 |
nicklas |
2049 |
<tr> |
| 3873 |
23 Oct 07 |
nicklas |
2050 |
<td>Affymetrix raw A.2</td> |
| 3873 |
23 Oct 07 |
nicklas |
2051 |
<td>Affymetrix</td> |
| 5699 |
16 Aug 11 |
nicklas |
2052 |
<td>Affymetrix scan A.2</td> |
| 5788 |
06 Oct 11 |
nicklas |
2053 |
<td>-</td> |
| 3873 |
23 Oct 07 |
nicklas |
2054 |
<td>Affymetrix A</td> |
| 3873 |
23 Oct 07 |
nicklas |
2055 |
<td>Feature extraction A</td> |
| 3873 |
23 Oct 07 |
nicklas |
2056 |
<td>Software A</td> |
| 5788 |
06 Oct 11 |
nicklas |
2057 |
<td><i>CEL file</i>: <code>affymetrix/E-TEST-1.ebi.ac.uk/jos1762.cel</code></td> |
| 3873 |
23 Oct 07 |
nicklas |
2058 |
</tr> |
| 3873 |
23 Oct 07 |
nicklas |
2059 |
<tr> |
| 3873 |
23 Oct 07 |
nicklas |
2060 |
<td>Affymetrix raw A.3</td> |
| 3873 |
23 Oct 07 |
nicklas |
2061 |
<td>Affymetrix</td> |
| 5699 |
16 Aug 11 |
nicklas |
2062 |
<td>Affymetrix scan A.3</td> |
| 5788 |
06 Oct 11 |
nicklas |
2063 |
<td>-</td> |
| 3873 |
23 Oct 07 |
nicklas |
2064 |
<td>Affymetrix A</td> |
| 3873 |
23 Oct 07 |
nicklas |
2065 |
<td>Feature extraction A</td> |
| 3873 |
23 Oct 07 |
nicklas |
2066 |
<td>Software A</td> |
| 5788 |
06 Oct 11 |
nicklas |
2067 |
<td><i>CEL file</i>: <code>affymetrix/E-TEST-1.ebi.ac.uk/jos1763.cel</code></td> |
| 3873 |
23 Oct 07 |
nicklas |
2068 |
</tr> |
| 5699 |
16 Aug 11 |
nicklas |
2069 |
<tr class="shaded"> |
| 5699 |
16 Aug 11 |
nicklas |
2070 |
<td>SeqRaw A.00h</td> |
| 5788 |
06 Oct 11 |
nicklas |
2071 |
<td>Sequencing/Expression-like/Cufflinks</td> |
| 5788 |
06 Oct 11 |
nicklas |
2072 |
<td>Arrangement A.00h</td> |
| 5699 |
16 Aug 11 |
nicklas |
2073 |
<td>Library A.00h</td> |
| 5788 |
06 Oct 11 |
nicklas |
2074 |
<td>RefSeqDesign A</td> |
| 5699 |
16 Aug 11 |
nicklas |
2075 |
<td>Cufflinks Settings A</td> |
| 5699 |
16 Aug 11 |
nicklas |
2076 |
<td>Cufflinks</td> |
| 5788 |
06 Oct 11 |
nicklas |
2077 |
<td><i>FPKM tracking file</i>: <code>sequencing/dataset1_norm1/isoforms.fpkm_tracking</code></td> |
| 5699 |
16 Aug 11 |
nicklas |
2078 |
</tr> |
| 5699 |
16 Aug 11 |
nicklas |
2079 |
<tr class="shaded"> |
| 5699 |
16 Aug 11 |
nicklas |
2080 |
<td>SeqRaw A.24h</td> |
| 5788 |
06 Oct 11 |
nicklas |
2081 |
<td>Sequencing/Expression-like/Cufflinks</td> |
| 5788 |
06 Oct 11 |
nicklas |
2082 |
<td>Arrangement A.24h</td> |
| 5699 |
16 Aug 11 |
nicklas |
2083 |
<td>Library A.24h</td> |
| 5788 |
06 Oct 11 |
nicklas |
2084 |
<td>RefSeqDesign A</td> |
| 5699 |
16 Aug 11 |
nicklas |
2085 |
<td>Cufflinks Settings A</td> |
| 5699 |
16 Aug 11 |
nicklas |
2086 |
<td>Cufflinks</td> |
| 5788 |
06 Oct 11 |
nicklas |
2087 |
<td><i>FPKM tracking file</i>: <code>sequencing/dataset2_norm1/isoforms.fpkm_tracking</code></td> |
| 5699 |
16 Aug 11 |
nicklas |
2088 |
</tr> |
| 2568 |
22 Aug 06 |
nicklas |
2089 |
</table> |
| 2568 |
22 Aug 06 |
nicklas |
2090 |
<p> |
| 2568 |
22 Aug 06 |
nicklas |
2091 |
</li> |
| 4789 |
24 Feb 09 |
nicklas |
2092 |
</ol> |
| 2568 |
22 Aug 06 |
nicklas |
2093 |
|
| 4789 |
24 Feb 09 |
nicklas |
2094 |
<a name="step3"></a> |
| 4789 |
24 Feb 09 |
nicklas |
2095 |
<h3>Third step</h3> |
| 4789 |
24 Feb 09 |
nicklas |
2096 |
<ol> |
| 4669 |
26 Nov 08 |
nicklas |
2097 |
<li> |
| 4669 |
26 Nov 08 |
nicklas |
2098 |
Create experiments: |
| 4669 |
26 Nov 08 |
nicklas |
2099 |
<table class="listing" cellspacing="0" cellpadding="2" border="0"> |
| 4669 |
26 Nov 08 |
nicklas |
2100 |
<tr> |
| 4669 |
26 Nov 08 |
nicklas |
2101 |
<th>Name</th> |
| 4669 |
26 Nov 08 |
nicklas |
2102 |
<th>Raw data type</th> |
| 4669 |
26 Nov 08 |
nicklas |
2103 |
<th>Raw bioassays</th> |
| 4669 |
26 Nov 08 |
nicklas |
2104 |
<th>Experimental factors</th> |
| 4669 |
26 Nov 08 |
nicklas |
2105 |
</tr> |
| 4669 |
26 Nov 08 |
nicklas |
2106 |
<tr> |
| 4669 |
26 Nov 08 |
nicklas |
2107 |
<td>Experiment A</td> |
| 4669 |
26 Nov 08 |
nicklas |
2108 |
<td>GenePix</td> |
| 4669 |
26 Nov 08 |
nicklas |
2109 |
<td>Raw bioassay A.00h,<br>Raw bioassay A.24h,<br>Raw bioassay A.00h (dye-swap),<br> |
| 4669 |
26 Nov 08 |
nicklas |
2110 |
Raw bioassay A.24h (dye-swap)</td> |
| 5983 |
23 Feb 12 |
nicklas |
2111 |
<td>Drug resistance, Time, RIN, Dye swap, PMT gain</td> |
| 4669 |
26 Nov 08 |
nicklas |
2112 |
</tr> |
| 4669 |
26 Nov 08 |
nicklas |
2113 |
<tr> |
| 4669 |
26 Nov 08 |
nicklas |
2114 |
<td>Affymetrix A</td> |
| 4669 |
26 Nov 08 |
nicklas |
2115 |
<td>Affymetrix</td> |
| 4669 |
26 Nov 08 |
nicklas |
2116 |
<td>Affymetrix raw A.1,<br>Affymetrix raw A.2,<br>Affymetrix raw A.3</td> |
| 5983 |
23 Feb 12 |
nicklas |
2117 |
<td>Drug resistance, Time, RIN, PMT gain</td> |
| 4669 |
26 Nov 08 |
nicklas |
2118 |
</tr> |
| 5699 |
16 Aug 11 |
nicklas |
2119 |
<tr> |
| 5699 |
16 Aug 11 |
nicklas |
2120 |
<td>Sequence A</td> |
| 5788 |
06 Oct 11 |
nicklas |
2121 |
<td>Cufflinks</td> |
| 5788 |
06 Oct 11 |
nicklas |
2122 |
<td>SeqRaw A.00h,<br>SeqRaw A.24h</td> |
| 5983 |
23 Feb 12 |
nicklas |
2123 |
<td>Drug resistance, Time, RIN</td> |
| 5699 |
16 Aug 11 |
nicklas |
2124 |
</tr> |
| 4669 |
26 Nov 08 |
nicklas |
2125 |
</table> |
| 4669 |
26 Nov 08 |
nicklas |
2126 |
<p> |
| 4669 |
26 Nov 08 |
nicklas |
2127 |
</li> |
| 4669 |
26 Nov 08 |
nicklas |
2128 |
|
| 2568 |
22 Aug 06 |
nicklas |
2129 |
<li> |
| 5788 |
06 Oct 11 |
nicklas |
2130 |
Import raw data to the Genepix and Cufflinks raw bioassays. |
| 5788 |
06 Oct 11 |
nicklas |
2131 |
There are two possible ways to do this: |
| 4669 |
26 Nov 08 |
nicklas |
2132 |
<ol> |
| 4669 |
26 Nov 08 |
nicklas |
2133 |
<li>Manually import to each raw bioassay. |
| 4669 |
26 Nov 08 |
nicklas |
2134 |
<li>Batch import to multiple raw bioassays. |
| 4669 |
26 Nov 08 |
nicklas |
2135 |
</ol> |
| 4669 |
26 Nov 08 |
nicklas |
2136 |
<p> |
| 4669 |
26 Nov 08 |
nicklas |
2137 |
<b>Manual import:</b> Go to the properties tab for each raw bioassay. |
| 4669 |
26 Nov 08 |
nicklas |
2138 |
Click on the <i>Import</i> button and use the auto-detect feature to |
| 4669 |
26 Nov 08 |
nicklas |
2139 |
import the raw data. Use the default configuration values except for |
| 4669 |
26 Nov 08 |
nicklas |
2140 |
those listed in the table below. |
| 4669 |
26 Nov 08 |
nicklas |
2141 |
<p> |
| 2751 |
20 Oct 06 |
nicklas |
2142 |
|
| 4669 |
26 Nov 08 |
nicklas |
2143 |
<b>Batch import:</b> The batch import is started from the |
| 4669 |
26 Nov 08 |
nicklas |
2144 |
properties tab of the <i>experiment</i>. Click on "Import" and |
| 5788 |
06 Oct 11 |
nicklas |
2145 |
use the auto-detect feature with one of the files from the raw bioassays. |
| 5788 |
06 Oct 11 |
nicklas |
2146 |
Use the default |
| 4669 |
26 Nov 08 |
nicklas |
2147 |
configuration values except for those listed in the table below. |
| 4669 |
26 Nov 08 |
nicklas |
2148 |
The batch import should import two raw data sets in one go (since it can |
| 4669 |
26 Nov 08 |
nicklas |
2149 |
only work with a single file format at a time and the dye-swap files uses |
| 4669 |
26 Nov 08 |
nicklas |
2150 |
a different file format). Repeat the batch import a second time to import |
| 4669 |
26 Nov 08 |
nicklas |
2151 |
the remaining two raw data sets. |
| 4669 |
26 Nov 08 |
nicklas |
2152 |
<p> |
| 4669 |
26 Nov 08 |
nicklas |
2153 |
|
| 2568 |
22 Aug 06 |
nicklas |
2154 |
<table class="listing" cellspacing="0" cellpadding="2" border="0"> |
| 2568 |
22 Aug 06 |
nicklas |
2155 |
<tr> |
| 4669 |
26 Nov 08 |
nicklas |
2156 |
<th>Parameter</th> |
| 4669 |
26 Nov 08 |
nicklas |
2157 |
<th>Value</th> |
| 4669 |
26 Nov 08 |
nicklas |
2158 |
<th>Mode</th> |
| 4669 |
26 Nov 08 |
nicklas |
2159 |
</tr> |
| 4669 |
26 Nov 08 |
nicklas |
2160 |
<tr> |
| 4669 |
26 Nov 08 |
nicklas |
2161 |
<td>Feature mismatch</td> |
| 4669 |
26 Nov 08 |
nicklas |
2162 |
<td>smart</td> |
| 4669 |
26 Nov 08 |
nicklas |
2163 |
<td>both</td> |
| 4669 |
26 Nov 08 |
nicklas |
2164 |
</tr> |
| 4669 |
26 Nov 08 |
nicklas |
2165 |
<tr> |
| 4669 |
26 Nov 08 |
nicklas |
2166 |
<td>Invalid numeric value</td> |
| 4669 |
26 Nov 08 |
nicklas |
2167 |
<td>null</td> |
| 4669 |
26 Nov 08 |
nicklas |
2168 |
<td>both</td> |
| 4669 |
26 Nov 08 |
nicklas |
2169 |
</tr> |
| 4669 |
26 Nov 08 |
nicklas |
2170 |
<tr> |
| 4669 |
26 Nov 08 |
nicklas |
2171 |
<td>Log file</td> |
| 4669 |
26 Nov 08 |
nicklas |
2172 |
<td>~/import.log</td> |
| 4669 |
26 Nov 08 |
nicklas |
2173 |
<td>batch import</td> |
| 4669 |
26 Nov 08 |
nicklas |
2174 |
</tr> |
| 4669 |
26 Nov 08 |
nicklas |
2175 |
</table> |
| 4669 |
26 Nov 08 |
nicklas |
2176 |
<p> |
| 4669 |
26 Nov 08 |
nicklas |
2177 |
|
| 4669 |
26 Nov 08 |
nicklas |
2178 |
In both cases, the import should produce the same results |
| 4669 |
26 Nov 08 |
nicklas |
2179 |
as in the table below. When using the batch import mode, the |
| 4669 |
26 Nov 08 |
nicklas |
2180 |
detailed information for each raw bioassay is only found in |
| 4669 |
26 Nov 08 |
nicklas |
2181 |
the log file. |
| 4669 |
26 Nov 08 |
nicklas |
2182 |
<table class="listing" cellspacing="0" cellpadding="2" border="0"> |
| 4669 |
26 Nov 08 |
nicklas |
2183 |
<tr> |
| 2568 |
22 Aug 06 |
nicklas |
2184 |
<th>Raw bioassay</th> |
| 2568 |
22 Aug 06 |
nicklas |
2185 |
<th>Raw data file</th> |
| 4246 |
24 Apr 08 |
nicklas |
2186 |
<th>Spots inserted/with null reporter/skipped)</th> |
| 4025 |
30 Nov 07 |
nicklas |
2187 |
<th>Annotations created</th> |
| 2568 |
22 Aug 06 |
nicklas |
2188 |
</tr> |
| 2568 |
22 Aug 06 |
nicklas |
2189 |
<tr> |
| 2568 |
22 Aug 06 |
nicklas |
2190 |
<td>Raw bioassay A.00h</td> |
| 2568 |
22 Aug 06 |
nicklas |
2191 |
<td>genepix.mouse.v4.37k.00h.gpr</td> |
| 4246 |
24 Apr 08 |
nicklas |
2192 |
<td>36,864/632/768</td> |
| 4025 |
30 Nov 07 |
nicklas |
2193 |
<td><i>Dye swap</i>: false</td> |
| 2568 |
22 Aug 06 |
nicklas |
2194 |
</tr> |
| 2568 |
22 Aug 06 |
nicklas |
2195 |
<tr> |
| 2568 |
22 Aug 06 |
nicklas |
2196 |
<td>Raw bioassay A.24h</td> |
| 2568 |
22 Aug 06 |
nicklas |
2197 |
<td>genepix.mouse.v4.37k.24h.gpr</td> |
| 4246 |
24 Apr 08 |
nicklas |
2198 |
<td>36,864/632/768</td> |
| 4025 |
30 Nov 07 |
nicklas |
2199 |
<td><i>Dye swap</i>: false</td> |
| 2568 |
22 Aug 06 |
nicklas |
2200 |
</tr> |
| 2568 |
22 Aug 06 |
nicklas |
2201 |
<tr class="shaded"> |
| 2568 |
22 Aug 06 |
nicklas |
2202 |
<td>Raw bioassay A.00h (dye-swap)</td> |
| 2568 |
22 Aug 06 |
nicklas |
2203 |
<td>genepix.mouse.v4.37k.00h.dyeswap.gpr</td> |
| 4246 |
24 Apr 08 |
nicklas |
2204 |
<td>36,864/632/768</td> |
| 4025 |
30 Nov 07 |
nicklas |
2205 |
<td><i>Dye swap</i>: true</td> |
| 2568 |
22 Aug 06 |
nicklas |
2206 |
</tr> |
| 2568 |
22 Aug 06 |
nicklas |
2207 |
<tr class="shaded"> |
| 2568 |
22 Aug 06 |
nicklas |
2208 |
<td>Raw bioassay A.24h (dye-swap)</td> |
| 2568 |
22 Aug 06 |
nicklas |
2209 |
<td>genepix.mouse.v4.37k.24h.dyeswap.gpr</td> |
| 4246 |
24 Apr 08 |
nicklas |
2210 |
<td>36,864/632/768</td> |
| 4025 |
30 Nov 07 |
nicklas |
2211 |
<td><i>Dye swap</i>: true</td> |
| 2568 |
22 Aug 06 |
nicklas |
2212 |
</tr> |
| 5788 |
06 Oct 11 |
nicklas |
2213 |
<tr> |
| 5788 |
06 Oct 11 |
nicklas |
2214 |
<td>SeqRaw A.00h</td> |
| 5788 |
06 Oct 11 |
nicklas |
2215 |
<td>dataset1_norm1/isoforms.fpkm_tracking</td> |
| 5788 |
06 Oct 11 |
nicklas |
2216 |
<td>38,293/0/0</td> |
| 5788 |
06 Oct 11 |
nicklas |
2217 |
<td>-</td> |
| 5788 |
06 Oct 11 |
nicklas |
2218 |
</tr> |
| 5788 |
06 Oct 11 |
nicklas |
2219 |
<tr> |
| 5788 |
06 Oct 11 |
nicklas |
2220 |
<td>SeqRaw A.24h</td> |
| 5788 |
06 Oct 11 |
nicklas |
2221 |
<td>dataset2_norm1/isoforms.fpkm_tracking</td> |
| 5788 |
06 Oct 11 |
nicklas |
2222 |
<td>38,293/0/0</td> |
| 5788 |
06 Oct 11 |
nicklas |
2223 |
<td>-</td> |
| 5788 |
06 Oct 11 |
nicklas |
2224 |
</tr> |
| 2568 |
22 Aug 06 |
nicklas |
2225 |
</table> |
| 2568 |
22 Aug 06 |
nicklas |
2226 |
<p> |
| 4669 |
26 Nov 08 |
nicklas |
2227 |
|
| 2568 |
22 Aug 06 |
nicklas |
2228 |
</li> |
| 2568 |
22 Aug 06 |
nicklas |
2229 |
|
| 6958 |
30 Sep 15 |
nicklas |
2230 |
<li><a name="inheritannotations"></a> |
| 6958 |
30 Sep 15 |
nicklas |
2231 |
Inherit the annotations from the scans, extracts, samples and biosource for each root raw bioassay. |
| 6958 |
30 Sep 15 |
nicklas |
2232 |
Use the <i>auto-inherit</i> function that exists on the experiment properties |
| 6958 |
30 Sep 15 |
nicklas |
2233 |
tab. Make sure that all experimental factors are selected by the check boxes, |
| 6958 |
30 Sep 15 |
nicklas |
2234 |
then click on the <i>Auto-inherit</i> link in the column header. Use the <b>Inherit</b> |
| 6958 |
30 Sep 15 |
nicklas |
2235 |
option for some annotations and <b>Clone</b> option for some. Uncheck the <b>No duplicates</b> |
| 6958 |
30 Sep 15 |
nicklas |
2236 |
option for the <i>RIN</i> annotation (see note 2 below). |
| 6958 |
30 Sep 15 |
nicklas |
2237 |
<br> |
| 6958 |
30 Sep 15 |
nicklas |
2238 |
<b>Note!</b> The <i>Affymetrix raw A.3</i> |
| 6958 |
30 Sep 15 |
nicklas |
2239 |
data set is missing biomaterial parents with annotations.<br> |
| 6958 |
30 Sep 15 |
nicklas |
2240 |
<b>Note 2!</b> In <i>Experiment A</i> there are duplicate values for the <i>RIN</i> |
| 6958 |
30 Sep 15 |
nicklas |
2241 |
annotations. Verify and fix this by manually removing the annotations that are inherited |
| 6958 |
30 Sep 15 |
nicklas |
2242 |
from the <i>Extract A.ref.qc</i> extract (value=9.2). |
| 6958 |
30 Sep 15 |
nicklas |
2243 |
<p> |
| 6958 |
30 Sep 15 |
nicklas |
2244 |
|
| 6958 |
30 Sep 15 |
nicklas |
2245 |
</li> |
| 6958 |
30 Sep 15 |
nicklas |
2246 |
|
| 6958 |
30 Sep 15 |
nicklas |
2247 |
|
| 2568 |
22 Aug 06 |
nicklas |
2248 |
<li> |
| 5788 |
06 Oct 11 |
nicklas |
2249 |
Check the experiment overview page and use the <b>Validate</b> function |
| 5788 |
06 Oct 11 |
nicklas |
2250 |
for each of the three experiments. |
| 5788 |
06 Oct 11 |
nicklas |
2251 |
<p> |
| 5788 |
06 Oct 11 |
nicklas |
2252 |
|
| 7052 |
11 Jan 16 |
nicklas |
2253 |
For the <b>Experiment A</b> experiment, it should display several warnings about missing |
| 7052 |
11 Jan 16 |
nicklas |
2254 |
kits and one warning about a missing biosurce on the reference sample. |
| 4025 |
30 Nov 07 |
nicklas |
2255 |
<p> |
| 5813 |
18 Oct 11 |
nicklas |
2256 |
The <b>Affymetrix A</b> experiment gives some more warnings. Most of them are |
| 4025 |
30 Nov 07 |
nicklas |
2257 |
related to not using the project default items, missing protocols |
| 4025 |
30 Nov 07 |
nicklas |
2258 |
and missing hardware. There should also be an error about missing |
| 4025 |
30 Nov 07 |
nicklas |
2259 |
experimental factor values for the <code>Affymetrix.3</code> |
| 4025 |
30 Nov 07 |
nicklas |
2260 |
raw bioassay. It is expected since this comes from the reference sample |
| 5813 |
18 Oct 11 |
nicklas |
2261 |
which doesn't have values for those annotations. The warnings about the |
| 5813 |
18 Oct 11 |
nicklas |
2262 |
number of spots mismatch is expected since the array design count probesets, |
| 5813 |
18 Oct 11 |
nicklas |
2263 |
while the raw bioassays count probes. |
| 4025 |
30 Nov 07 |
nicklas |
2264 |
<p> |
| 4025 |
30 Nov 07 |
nicklas |
2265 |
|
| 5813 |
18 Oct 11 |
nicklas |
2266 |
The <b>Sequence A</b> experiment also has some missing items, and a different |
| 5813 |
18 Oct 11 |
nicklas |
2267 |
raw data type for the experiment and raw bioassays. |
| 5788 |
06 Oct 11 |
nicklas |
2268 |
|
| 5788 |
06 Oct 11 |
nicklas |
2269 |
<p> |
| 4025 |
30 Nov 07 |
nicklas |
2270 |
Change validation options to reduce the number of warnings: |
| 4025 |
30 Nov 07 |
nicklas |
2271 |
<table class="listing" cellspacing="0" cellpadding="2" border="0"> |
| 4025 |
30 Nov 07 |
nicklas |
2272 |
<tr> |
| 4025 |
30 Nov 07 |
nicklas |
2273 |
<th>Validation option</th> |
| 4025 |
30 Nov 07 |
nicklas |
2274 |
<th>Setting</th> |
| 4025 |
30 Nov 07 |
nicklas |
2275 |
</tr> |
| 4025 |
30 Nov 07 |
nicklas |
2276 |
<tr> |
| 4025 |
30 Nov 07 |
nicklas |
2277 |
<td>Project defaults</td> |
| 4025 |
30 Nov 07 |
nicklas |
2278 |
<td>Set all to <code>Ignore</code></td> |
| 4025 |
30 Nov 07 |
nicklas |
2279 |
</tr> |
| 4025 |
30 Nov 07 |
nicklas |
2280 |
<tr> |
| 4025 |
30 Nov 07 |
nicklas |
2281 |
<td>Missing items</td> |
| 4025 |
30 Nov 07 |
nicklas |
2282 |
<td>Set all to <code>Ignore</code></td> |
| 4025 |
30 Nov 07 |
nicklas |
2283 |
</tr> |
| 4025 |
30 Nov 07 |
nicklas |
2284 |
<tr> |
| 4025 |
30 Nov 07 |
nicklas |
2285 |
<td>Annotations - Missing factor value</td> |
| 4025 |
30 Nov 07 |
nicklas |
2286 |
<td><code>Warning</code></td> |
| 4025 |
30 Nov 07 |
nicklas |
2287 |
</tr> |
| 5091 |
31 Aug 09 |
nicklas |
2288 |
<tr> |
| 5091 |
31 Aug 09 |
nicklas |
2289 |
<td>Other - Raw spots <> features</td> |
| 5091 |
31 Aug 09 |
nicklas |
2290 |
<td><code>Ignore</code></td> |
| 5091 |
31 Aug 09 |
nicklas |
2291 |
</tr> |
| 4025 |
30 Nov 07 |
nicklas |
2292 |
</table> |
| 4025 |
30 Nov 07 |
nicklas |
2293 |
|
| 4025 |
30 Nov 07 |
nicklas |
2294 |
After the changes there should now only be two warnings about the |
| 5813 |
18 Oct 11 |
nicklas |
2295 |
missing factor values for the Affymetrix experiment and no warnings |
| 5813 |
18 Oct 11 |
nicklas |
2296 |
at all for the other experiments. |
| 4025 |
30 Nov 07 |
nicklas |
2297 |
|
| 4025 |
30 Nov 07 |
nicklas |
2298 |
<p> |
| 4025 |
30 Nov 07 |
nicklas |
2299 |
</li> |
| 4025 |
30 Nov 07 |
nicklas |
2300 |
|
| 2568 |
22 Aug 06 |
nicklas |
2301 |
</ol> |
| 2568 |
22 Aug 06 |
nicklas |
2302 |
|
| 2568 |
22 Aug 06 |
nicklas |
2303 |
<a name="analysis"></a> |
| 2568 |
22 Aug 06 |
nicklas |
2304 |
<h2>6. Analysis tests</h2> |
| 2568 |
22 Aug 06 |
nicklas |
2305 |
<p> |
| 2568 |
22 Aug 06 |
nicklas |
2306 |
Now it is time to analyse the data. The analysis test should be done |
| 2568 |
22 Aug 06 |
nicklas |
2307 |
by both a regular user and a guest. |
| 2568 |
22 Aug 06 |
nicklas |
2308 |
</p> |
| 2568 |
22 Aug 06 |
nicklas |
2309 |
|
| 2568 |
22 Aug 06 |
nicklas |
2310 |
<ol> |
| 2568 |
22 Aug 06 |
nicklas |
2311 |
<li> |
| 2568 |
22 Aug 06 |
nicklas |
2312 |
Activate the <code>Project A</code> project<p> |
| 2568 |
22 Aug 06 |
nicklas |
2313 |
</li> |
| 2568 |
22 Aug 06 |
nicklas |
2314 |
|
| 2568 |
22 Aug 06 |
nicklas |
2315 |
<li> |
| 5886 |
23 Nov 11 |
nicklas |
2316 |
Go to the <code>Experiment A</code> experiment. |
| 2568 |
22 Aug 06 |
nicklas |
2317 |
<p> |
| 2568 |
22 Aug 06 |
nicklas |
2318 |
</li> |
| 2568 |
22 Aug 06 |
nicklas |
2319 |
|
| 2568 |
22 Aug 06 |
nicklas |
2320 |
<li> |
| 5886 |
23 Nov 11 |
nicklas |
2321 |
Clone the reporters: |
| 2568 |
22 Aug 06 |
nicklas |
2322 |
<table class="listing" cellspacing="0" cellpadding="2" border="0"> |
| 2568 |
22 Aug 06 |
nicklas |
2323 |
<tr> |
| 5886 |
23 Nov 11 |
nicklas |
2324 |
<th>Clone template</th> |
| 5886 |
23 Nov 11 |
nicklas |
2325 |
<th>Clone source</th> |
| 5886 |
23 Nov 11 |
nicklas |
2326 |
</tr> |
| 5886 |
23 Nov 11 |
nicklas |
2327 |
<tr> |
| 5886 |
23 Nov 11 |
nicklas |
2328 |
<td>Template A</td> |
| 5886 |
23 Nov 11 |
nicklas |
2329 |
<td>Raw data</td> |
| 5886 |
23 Nov 11 |
nicklas |
2330 |
</tr> |
| 5886 |
23 Nov 11 |
nicklas |
2331 |
</table> |
| 5886 |
23 Nov 11 |
nicklas |
2332 |
Click on "Next" and wait for the plug-in to finish. It should |
| 5886 |
23 Nov 11 |
nicklas |
2333 |
report that 35,912 reporters has been cloned. |
| 5886 |
23 Nov 11 |
nicklas |
2334 |
<p> |
| 5886 |
23 Nov 11 |
nicklas |
2335 |
</li> |
| 5886 |
23 Nov 11 |
nicklas |
2336 |
|
| 5886 |
23 Nov 11 |
nicklas |
2337 |
<li> |
| 5886 |
23 Nov 11 |
nicklas |
2338 |
Switch to the "Bioassay sets" tab. Create a new root bioassay set: |
| 5886 |
23 Nov 11 |
nicklas |
2339 |
<table class="listing" cellspacing="0" cellpadding="2" border="0"> |
| 5886 |
23 Nov 11 |
nicklas |
2340 |
<tr> |
| 2568 |
22 Aug 06 |
nicklas |
2341 |
<th>Bioassay set name</th> |
| 2568 |
22 Aug 06 |
nicklas |
2342 |
<th>Raw bioassays</th> |
| 2568 |
22 Aug 06 |
nicklas |
2343 |
<th>Formula</th> |
| 2568 |
22 Aug 06 |
nicklas |
2344 |
</tr> |
| 2568 |
22 Aug 06 |
nicklas |
2345 |
<tr> |
| 2568 |
22 Aug 06 |
nicklas |
2346 |
<td>Root bioassay set</td> |
| 2568 |
22 Aug 06 |
nicklas |
2347 |
<td>all</td> |
| 2568 |
22 Aug 06 |
nicklas |
2348 |
<td>Mean FG - Mean BG</td> |
| 2568 |
22 Aug 06 |
nicklas |
2349 |
</tr> |
| 2568 |
22 Aug 06 |
nicklas |
2350 |
</table> |
| 2682 |
02 Oct 06 |
jari |
2351 |
Wait for the plug-in to finish. |
| 2568 |
22 Aug 06 |
nicklas |
2352 |
<p> |
| 2568 |
22 Aug 06 |
nicklas |
2353 |
</li> |
| 2568 |
22 Aug 06 |
nicklas |
2354 |
|
| 2568 |
22 Aug 06 |
nicklas |
2355 |
<li> |
| 2568 |
22 Aug 06 |
nicklas |
2356 |
Select the created bioassay set and create a filtered bioassayset: |
| 2568 |
22 Aug 06 |
nicklas |
2357 |
<table class="listing" cellspacing="0" cellpadding="2" border="0"> |
| 2568 |
22 Aug 06 |
nicklas |
2358 |
<tr> |
| 2568 |
22 Aug 06 |
nicklas |
2359 |
<th>Child name</th> |
| 2568 |
22 Aug 06 |
nicklas |
2360 |
<th>Filter preset</th> |
| 2568 |
22 Aug 06 |
nicklas |
2361 |
<th>Expression</th> |
| 2568 |
22 Aug 06 |
nicklas |
2362 |
</tr> |
| 2568 |
22 Aug 06 |
nicklas |
2363 |
<tr> |
| 2568 |
22 Aug 06 |
nicklas |
2364 |
<td>Filtered bioassay set</td> |
| 4298 |
13 May 08 |
nicklas |
2365 |
<td>-</td> |
| 4246 |
24 Apr 08 |
nicklas |
2366 |
<td>ch(1) > 0 && ch(2) > 0 && rep('id') != null</td> |
| 2568 |
22 Aug 06 |
nicklas |
2367 |
</tr> |
| 2568 |
22 Aug 06 |
nicklas |
2368 |
</table> |
| 2682 |
02 Oct 06 |
jari |
2369 |
Wait for the plug-in to finish. It should report that 136,498 spots remain and |
| 4246 |
24 Apr 08 |
nicklas |
2370 |
that 10,958 spots has been removed. |
| 2568 |
22 Aug 06 |
nicklas |
2371 |
<p> |
| 2568 |
22 Aug 06 |
nicklas |
2372 |
</li> |
| 2568 |
22 Aug 06 |
nicklas |
2373 |
|
| 2568 |
22 Aug 06 |
nicklas |
2374 |
<li> |
| 2682 |
02 Oct 06 |
jari |
2375 |
Select the filtered bioassay set and run a normalization plug-in: |
| 2568 |
22 Aug 06 |
nicklas |
2376 |
<table class="listing" cellspacing="0" cellpadding="2" border="0"> |
| 2568 |
22 Aug 06 |
nicklas |
2377 |
<tr> |
| 2568 |
22 Aug 06 |
nicklas |
2378 |
<th>Plugin</th> |
| 2568 |
22 Aug 06 |
nicklas |
2379 |
<th>Parameters</th> |
| 2568 |
22 Aug 06 |
nicklas |
2380 |
</tr> |
| 2568 |
22 Aug 06 |
nicklas |
2381 |
<tr> |
| 2568 |
22 Aug 06 |
nicklas |
2382 |
<td>Normalization: Lowess</td> |
| 4789 |
24 Feb 09 |
nicklas |
2383 |
<td>Accept the default parameters.</td> |
| 2568 |
22 Aug 06 |
nicklas |
2384 |
</tr> |
| 2568 |
22 Aug 06 |
nicklas |
2385 |
</table> |
| 2751 |
20 Oct 06 |
nicklas |
2386 |
Wait for the plug in to finish. It should report that 136,498 spots has been |
| 2751 |
20 Oct 06 |
nicklas |
2387 |
normalized and 0 spots has been removed. |
| 2568 |
22 Aug 06 |
nicklas |
2388 |
<p> |
| 2568 |
22 Aug 06 |
nicklas |
2389 |
</li> |
| 2568 |
22 Aug 06 |
nicklas |
2390 |
|
| 2568 |
22 Aug 06 |
nicklas |
2391 |
<li> |
| 5091 |
31 Aug 09 |
nicklas |
2392 |
Select the normalized bioassay set and check the MA plots and |
| 2568 |
22 Aug 06 |
nicklas |
2393 |
the correction factor plots. Here are four examples: |
| 2568 |
22 Aug 06 |
nicklas |
2394 |
<table class="listing" cellspacing="0" cellpadding="2" border="0"> |
| 2568 |
22 Aug 06 |
nicklas |
2395 |
<tr> |
| 5091 |
31 Aug 09 |
nicklas |
2396 |
<th>MA plots</th> |
| 2568 |
22 Aug 06 |
nicklas |
2397 |
<th>Correction factor plots</th> |
| 2568 |
22 Aug 06 |
nicklas |
2398 |
</tr> |
| 2568 |
22 Aug 06 |
nicklas |
2399 |
<tr> |
| 2568 |
22 Aug 06 |
nicklas |
2400 |
<td><img src="overview.png"><br><img src="overview.dyeswap.png"></td> |
| 2568 |
22 Aug 06 |
nicklas |
2401 |
<td><img src="correction.png"><br><img src="correction.dyeswap.png"></td> |
| 2568 |
22 Aug 06 |
nicklas |
2402 |
</tr> |
| 2568 |
22 Aug 06 |
nicklas |
2403 |
</table> |
| 2568 |
22 Aug 06 |
nicklas |
2404 |
<p> |
| 2568 |
22 Aug 06 |
nicklas |
2405 |
</li> |
| 2568 |
22 Aug 06 |
nicklas |
2406 |
|
| 2568 |
22 Aug 06 |
nicklas |
2407 |
<li> |
| 2568 |
22 Aug 06 |
nicklas |
2408 |
Try the plot tool with the following plots. Use the <code>Save</code> function |
| 2568 |
22 Aug 06 |
nicklas |
2409 |
to save one them as a file in the BASE file system, and the <code>Download</code> |
| 2568 |
22 Aug 06 |
nicklas |
2410 |
function to download a plot to your computer. |
| 2568 |
22 Aug 06 |
nicklas |
2411 |
<table class="listing" cellspacing="0" cellpadding="2" border="0"> |
| 2568 |
22 Aug 06 |
nicklas |
2412 |
<tr> |
| 2568 |
22 Aug 06 |
nicklas |
2413 |
<th>Plot type</th> |
| 2594 |
24 Aug 06 |
martin |
2414 |
<th>Y-axis preset</th> |
| 2568 |
22 Aug 06 |
nicklas |
2415 |
<th>X-axis preset</th> |
| 2568 |
22 Aug 06 |
nicklas |
2416 |
<th>Other options</th> |
| 2568 |
22 Aug 06 |
nicklas |
2417 |
</tr> |
| 2568 |
22 Aug 06 |
nicklas |
2418 |
<tr> |
| 2568 |
22 Aug 06 |
nicklas |
2419 |
<td>Scatter plot</td> |
| 2568 |
22 Aug 06 |
nicklas |
2420 |
<td>M, log2(ch1 / ch2)</td> |
| 2568 |
22 Aug 06 |
nicklas |
2421 |
<td>A, log10(ch1 * ch2) / 2</td> |
| 2568 |
22 Aug 06 |
nicklas |
2422 |
<td>-</td> |
| 2568 |
22 Aug 06 |
nicklas |
2423 |
</tr> |
| 2568 |
22 Aug 06 |
nicklas |
2424 |
<tr> |
| 2568 |
22 Aug 06 |
nicklas |
2425 |
<td>Histogram plot</td> |
| 2568 |
22 Aug 06 |
nicklas |
2426 |
<td>Count</td> |
| 2568 |
22 Aug 06 |
nicklas |
2427 |
<td>Ratio, ch1 / ch2</td> |
| 2568 |
22 Aug 06 |
nicklas |
2428 |
<td> |
| 2568 |
22 Aug 06 |
nicklas |
2429 |
<table border="0" cellspacing="0" cellpadding="2"> |
| 2568 |
22 Aug 06 |
nicklas |
2430 |
<tr> |
| 2568 |
22 Aug 06 |
nicklas |
2431 |
<td><i>Log scale</i></td> |
| 2568 |
22 Aug 06 |
nicklas |
2432 |
<td>checked</td> |
| 2568 |
22 Aug 06 |
nicklas |
2433 |
</tr> |
| 2568 |
22 Aug 06 |
nicklas |
2434 |
<tr> |
| 2568 |
22 Aug 06 |
nicklas |
2435 |
<td><i>Bin size</i></td> |
| 2568 |
22 Aug 06 |
nicklas |
2436 |
<td>0.1</td> |
| 2568 |
22 Aug 06 |
nicklas |
2437 |
</tr> |
| 2769 |
23 Oct 06 |
nicklas |
2438 |
<tr> |
| 2769 |
23 Oct 06 |
nicklas |
2439 |
<td><i>Annotation</i></td> |
| 4669 |
26 Nov 08 |
nicklas |
2440 |
<td>Time</td> |
| 2769 |
23 Oct 06 |
nicklas |
2441 |
</tr> |
| 2568 |
22 Aug 06 |
nicklas |
2442 |
</table> |
| 2568 |
22 Aug 06 |
nicklas |
2443 |
</td> |
| 2568 |
22 Aug 06 |
nicklas |
2444 |
</tr> |
| 2568 |
22 Aug 06 |
nicklas |
2445 |
</table> |
| 2568 |
22 Aug 06 |
nicklas |
2446 |
<p> |
| 2568 |
22 Aug 06 |
nicklas |
2447 |
Here are two examples: |
| 2568 |
22 Aug 06 |
nicklas |
2448 |
<table class="listing" cellspacing="0" cellpadding="2" border="0"> |
| 2568 |
22 Aug 06 |
nicklas |
2449 |
<tr> |
| 2568 |
22 Aug 06 |
nicklas |
2450 |
<th>Scatter plot</th> |
| 2568 |
22 Aug 06 |
nicklas |
2451 |
</tr> |
| 2568 |
22 Aug 06 |
nicklas |
2452 |
<tr> |
| 2568 |
22 Aug 06 |
nicklas |
2453 |
<td><img src="scatter.png"></td> |
| 2568 |
22 Aug 06 |
nicklas |
2454 |
</tr> |
| 2568 |
22 Aug 06 |
nicklas |
2455 |
</table> |
| 2568 |
22 Aug 06 |
nicklas |
2456 |
<p> |
| 2568 |
22 Aug 06 |
nicklas |
2457 |
<table class="listing" cellspacing="0" cellpadding="2" border="0"> |
| 2568 |
22 Aug 06 |
nicklas |
2458 |
<tr> |
| 2568 |
22 Aug 06 |
nicklas |
2459 |
<th>Histogram plot</th> |
| 2568 |
22 Aug 06 |
nicklas |
2460 |
</tr> |
| 2568 |
22 Aug 06 |
nicklas |
2461 |
<tr> |
| 2568 |
22 Aug 06 |
nicklas |
2462 |
<td><img src="histogram.png"></td> |
| 2568 |
22 Aug 06 |
nicklas |
2463 |
</tr> |
| 2568 |
22 Aug 06 |
nicklas |
2464 |
</table> |
| 2568 |
22 Aug 06 |
nicklas |
2465 |
<p> |
| 2568 |
22 Aug 06 |
nicklas |
2466 |
</li> |
| 2568 |
22 Aug 06 |
nicklas |
2467 |
|
| 2568 |
22 Aug 06 |
nicklas |
2468 |
</ol> |
| 2568 |
22 Aug 06 |
nicklas |
2469 |
|
| 2568 |
22 Aug 06 |
nicklas |
2470 |
|
| 2568 |
22 Aug 06 |
nicklas |
2471 |
</body> |
| 2568 |
22 Aug 06 |
nicklas |
2472 |
</html> |