source: trunk/doc/test/roles/index.html @ 4548

Last change on this file since 4548 was 4548, checked in by Nicklas Nordborg, 13 years ago

References #792: Add support for units to annotation values

Display/use annotation with units in the following places:

  • Experimental factors for an experiment
  • Experiment overview
  • Plot tool
  • Experiment explorer
  • Roles test program
  • Table exporter
  • Property svn:eol-style set to native
  • Property svn:keywords set to Date Id
File size: 41.4 KB
Line 
1<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
2<!--
3  $Id: index.html 4548 2008-09-26 12:29:03Z nicklas $
4
5  Copyright (C) 2006 Jari Hakkinen, Nicklas Nordborg, Martin Svensson
6
7  This file is part of BASE - BioArray Software Environment.
8  Available at http://base.thep.lu.se/
9
10  BASE is free software; you can redistribute it and/or
11  modify it under the terms of the GNU General Public License
12  as published by the Free Software Foundation; either version 3
13  of the License, or (at your option) any later version.
14
15  BASE is distributed in the hope that it will be useful,
16  but WITHOUT ANY WARRANTY; without even the implied warranty of
17  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
18  GNU General Public License for more details.
19
20  You should have received a copy of the GNU General Public License
21  along with BASE. If not, see <http://www.gnu.org/licenses/>.
22-->
23<html>
24  <head>
25    <title>BASE - Test procedures for predefined roles</title>
26  <link rel=stylesheet type="text/css" href="../../styles.css">
27  </head>
28<body>
29
30<div class="navigation">
31  <a href="../../index.html">BASE</a>
32  <img src="../../next.gif">
33  <a href="../index.html">Test procedures</a>
34  <img src="../../next.gif">
35  Predefined roles
36</div>
37
38  <h1>Test procedures for predefined roles</h1>
39
40  <div class="abstract">
41    <p>
42      This document defines a procedure for testing that
43      the predefined roles can perform their work as intended. The main
44      purpose is to weed out permission problems resulting from:
45    </p>
46   
47    <ul>
48    <li>Incorrect permissions installed by installation program</li>
49    <li>Bugs in the permission handling in the core</li>
50    <li>Incorrect handling of permissions in the web client</li>
51    </ul>
52   
53    <p>
54      The test procedure also tests that the
55      basic functionality is working:
56    </p>
57   
58    <ul>
59      <li>Creating items and linking them to other items</li>
60      <li>Defining import file formats</li>
61      <li>Importing array LIMS data</li>
62      <li>Importing and validating raw data against array LIMS data</li>
63      <li>Running analysis plug-ins</li>
64      <li>Using files instead of the database for storing data</li>
65    </ul>
66   
67    <b>Contents</b><br>
68    <ol>
69    <li><a href="#summary">Summary of the test procedure</a></li>
70    <li><a href="#root">Root user tests</a></li>
71    <li><a href="#admin">Administrator tests</a></li>
72    <li><a href="#power">Power user tests</a></li>
73    <li><a href="#user">User tests</a></li>
74    <li><a href="#analysis">Analysis tests</a></li>
75    </ol>
76   
77    <p class="authors">
78    <b>Last updated:</b> $Date: 2008-09-26 12:29:03 +0000 (Fri, 26 Sep 2008) $
79    </p>
80  </div>
81
82 
83  <a name="summary"></a>
84  <h2>1. Summary of the test procedure</h2>
85
86  <p>
87    Here is a summary of the test procedure:
88  </p>
89
90  <ol>
91  <li>Always start with a fresh installation.</li>
92 
93  <li>The root user creates an administrator.</li>
94 
95  <li>The administrator creates more users and some global resources:
96    <ul>
97    <li>A group and three other users. One power user, one user and one guest.</li>
98    <li>File formats for importing reporters</li>
99    <li>Imports reporters</li>
100    </ul>
101  </li>
102   
103  <li>The power user creates item related to the project management:
104    <ul>
105    <li>A project</li>
106    <li>Protocols, one for each type of action: sampling, extraction, etc.</li>
107    <li>Hardware and software that are used in the project</li>
108    <li>Annotation types for annotations used in the project</li>
109    <li>File formats for importing plates, print maps and raw data</li>
110    <li>LIMS information - plate type, plates, array design, array batch and array slides</li>
111    </ul>
112  </li>
113 
114  <li>The user creates items related to an actual experiment:
115    <ul>
116    <li>Biomaterials: biosources, samples, extracts, etc.</li>
117    <li>Experiment: hybridizations, scans, images, raw bioassays</li>
118    <li>Import raw data</li>
119    </ul>
120  </li>
121 
122  <li>Both the user and the guest then do some analysis:
123    <ul>
124    <li>Create a root bioassay set</li>
125    <li>Filter the bioassay set</li>
126    <li>Run a normalization plug-in</li>
127    <li>Check the result by listing and plotting the data</li>
128    </ul>
129  </li>
130  </ol>
131
132  <p>
133    These tests can also be run in automated mode by test programs. This will of
134    course not test the web client, but are useful if one quickly needs to do
135    parts of the test and then continue with, for example, the user or analysis tests
136    on the web.
137  </p>
138 
139  <p>
140    The data files needed by the tests are NOT included in the subversion repository.
141    The main reason is that they are too large, and that we don't have permission to
142    make them publicly available for download. To get the test file you need to be a
143    core developer. Read the instructions on the
144    <a href="http://base.thep.lu.se/wiki/DeveloperInformation">DeveloperInformation</a>
145    page, <code>Test data</code> section on the Base 2 web site. The automated
146    test programs require that file are placed (checked out) in the 'testdata'
147    directory located in the BASE root directory. NOTE! Some test data files are
148    bzip-compressed. These need to be uncompressed before they are uploaded to BASE.
149  </p>
150 
151  <p>
152    To run the tests do the following:
153  </p>
154  <ol>
155   
156    <li>Compile the core and the test programs: <code>ant main test</code>.</li>
157
158    <li>Change to the <code>build/test/</code> directory.</li>
159
160    <li>Run test programs: <code>./test.sh roles &lt;cmds&gt;</code> where
161      <code>&lt;cmds&gt;</code> is one or more of the following:
162      <ul>
163      <li><code>all</code>: run all tests</li>
164      <li><code>root</code>: run the root user tests</li>
165      <li><code>admin</code>: run the administrator tests</li>
166      <li><code>power</code>: run the power user tests</li>
167      <li><code>user</code>: run the regular user tests</li>
168      <li><code>guest</code>: run the guest user tests</li>
169      </ul>
170    </li>
171   
172  </ol>
173   
174  <a name="root"></a>
175  <h2>2. Root user tests</h2>
176  <p>
177    The root user creates an administrator which is a server-wide admin.
178  </p>
179 
180  <ol>
181  <li>
182    Create a new user and set the following
183    properties. All other properties may remain unchanged.
184   
185    <table class="listing" cellspacing="0" cellpadding="2" border="0">
186    <tr>
187      <th>Name</th>
188      <th>Login/Password</th>
189      <th>Quota</th>
190      <th>Quota group</th>
191      <th>Membership</th>
192    </tr>
193    <tr>
194      <td>Admin</td>
195      <td>admin/admin</td>
196      <td>Unlimited</td>
197      <td>-</td>
198      <td>Roles: Administrator</td>
199    </tr>
200    </table>
201  </li>
202  </ol>
203
204  <a name="admin"></a>
205  <h2>3. Administrator tests</h2>
206  <p>
207    The administrator creates users for a project and gives them permissions
208    that are suitable for their role in the project. The administrator also
209    sets up quota and group membership.
210  </p>
211
212  <ol>
213  <li>
214    Create a new group and set the following properties:
215 
216    <table class="listing" cellspacing="0" cellpadding="2" border="0">
217    <tr>
218      <th>Name</th>
219      <th>Quota</th>
220    </tr>
221    <tr>
222      <td>Group A</td>
223      <td>1GB</td>
224    </tr>
225    </table>
226    <p>
227  </li>
228 
229  <li>
230    Create the following users:
231
232    <table class="listing" cellspacing="0" cellpadding="2" border="0">
233    <tr>
234      <th>Name</th>
235      <th>Login/Password</th>
236      <th>Quota</th>
237      <th>Quota group</th>
238      <th>Membership</th>
239      <th>Other</th>
240    </tr>
241    <tr>
242      <td>Power user</td>
243      <td>power/power</td>
244      <td>1GB</td>
245      <td>Group A</td>
246      <td>Roles: Power user</td>
247      <td>-</td>
248    </tr>
249    <tr>
250      <td>User</td>
251      <td>user/user</td>
252      <td>1GB</td>
253      <td>Group A</td>
254      <td>Roles: User</td>
255      <td>-</td>
256    </tr>
257    <tr>
258      <td>Guest</td>
259      <td>guest/guest</td>
260      <td>10MB</td>
261      <td>Group A</td>
262      <td>Roles: Guest</td>
263      <td><i>Multi-user account</i> checked</td>
264    </tr>
265    </table>
266    <p>
267  </li>
268 
269  <li>Give USE permission for the listed users to the following plugins:
270 
271    <table class="listing" cellspacing="0" cellpadding="2" border="0">
272    <tr>
273      <th>User</th>
274      <th>Plugins</th>
275    </tr>
276    <tr>
277      <td>Power user</td>
278      <td>
279        <ul>
280        <li>Plate importer</li>
281        <li>Reporter map importer</li>
282        <li>Print map importer</li>
283        </ul>
284      </td>
285    </tr>
286    </table>
287    <p>
288  </li>
289
290  <li>
291    Create file formats (<i>i.e.</i>, plug-in configurations) for importing
292    reporters. The formats marked as
293    optional are not used in the test procedure, but may be useful to weed
294    out import problems, since they allow importing all info from the raw
295    data files. You may either enter the regular expressions as specified or
296    use the "Test with file" feature.
297   
298    <table class="listing" cellspacing="0" cellpadding="2" border="0">
299    <tr>
300      <th>Name</th>
301      <th>Plugin</th>
302      <th>Configuration values</th>
303    </tr>
304    <tr class="oddrow">
305      <td>Reporters for project A</td>
306      <td>Reporter importer</td>
307      <td>
308      <b>Test with file:</b> <code>plates_and_reporters.mouse.v4.37k.txt</code>
309      <table border="0" cellspacing="0" cellpadding="2">
310      <tr>
311        <td><i>Data header</i></td>
312        <td>384_number\t384_column\t384_row\t384_position\toligo_id.*</td>
313      </tr>
314      <tr>
315        <td><i>Data splitter</i></td>
316        <td>\t</td>
317      </tr>
318      <tr>
319        <td><i>Min data columns</i></td>
320        <td>5</td>
321      </tr>
322      <tr>
323        <td><i>Name</i></td>
324        <td>\oligo_id\</td>
325      </tr>
326      <tr>
327        <td><i>Reporter ID</i></td>
328        <td>\oligo_id\</td>
329      </tr>
330      <tr>
331        <td><i>Description</i></td>
332        <td>\description_Ensembl*\</td>
333      </tr>
334      <tr>
335        <td><i>Gene symbol</i></td>
336        <td>\gene_symbol_Ensembl*\</td>
337      </tr>
338      <tr>
339        <td><i>Sequence</i></td>
340        <td>\oligo_sequence\</td>
341      </tr>
342      </table>
343     
344      </td>
345    </tr>
346   
347    <tr class="evenrow">
348      <td>GenePix reporter importer<br>(optional)</td>
349      <td>Reporter importer</td>
350      <td>
351
352      <b>Test with file:</b> <code>genepix.mouse.v4.37k.00h.gpr</code>
353      <table border="0" cellspacing="0" cellpadding="2">
354      <tr>
355        <td><i>Data header</i></td>
356        <td>"Block"\t"Column"\t"Row"\t"Name"\t"ID"\t.*</td>
357      </tr>
358      <tr>
359        <td><i>Data splitter</i></td>
360        <td>\t</td>
361      </tr>
362      <tr>
363        <td><i>Min data columns</i></td>
364        <td>48</td>
365      </tr>
366      <tr>
367        <td><i>Max data columns</i></td>
368        <td>48</td>
369      </tr>
370      <tr>
371        <td><i>Name</i></td>
372        <td>\Name\</td>
373      </tr>
374      <tr>
375        <td><i>Reporter ID</i></td>
376        <td>\ID\</td>
377      </tr>
378      </table>
379
380      </td>
381    </tr>
382    <tr class="oddrow">
383      <td>Reporters from Affymetrix annotations file</td>
384      <td>Reporter importer</td>
385      <td>
386      <b>Test with file:</b> <code>MG_U74Av2_annot.csv.bz2</code>
387      <table border="0" cellspacing="0" cellpadding="2">
388      <tr>
389        <td><i>Data header</i></td>
390        <td>"Probe Set ID","GeneChip Array".*</td>
391      </tr>
392      <tr>
393        <td><i>Data splitter</i></td>
394        <td>(?!"),(?=")</td>
395      </tr>
396      <tr>
397        <td><i>Name</i></td>
398        <td>\Probe Set ID\</td>
399      </tr>
400      <tr>
401        <td><i>Reporter ID</i></td>
402        <td>\Probe Set ID\</td>
403      </tr>
404      <tr>
405        <td><i>Description</i></td>
406        <td>\Target Description\</td>
407      </tr>
408      <tr>
409        <td><i>Gene symbol</i></td>
410        <td>\Gene Symbol\</td>
411      </tr>
412      </table>
413     
414      </td>
415    </tr>   
416    </table>
417    <p>
418    </li>
419
420    <li>
421      Import reporters:
422      <ol>
423      <li>Go to the <code>View -> Reporters</code> page.</li>
424      <li>Click on the <code>Import</code> button.</li>
425      <li>Choose <code>auto-detect</code> and then upload
426        the file <code>plates_and_reporters.mouse.v4.37k.txt</code>.</li>
427      <li>The <code>Reporters for project A</code> format should be
428        found.</li>
429      <li>Select the <code>skip</code> option for the "Missing a required" value
430        since the file contains rows with empty reporter ID:s.
431      <li>Continue and wait for the import to finish. It should create 35,912 new reporters.</li>
432      <li>
433        Repeat the procedure with the <code>MG_U74Av2_annot.csv</code> file. This time
434        also select <code>crop</code> for the "String too long" setting since
435        the file contains data that is too large for the datbase.
436        12,488 new reporters should be created.
437      </ol>
438      <p>
439 
440    </li>
441
442
443  </ol>
444
445
446  <a name="power"></a>
447  <h2>4. Power user tests</h2>
448  <p>
449    The power user is the typical owner/administrator of a project. The power user sets
450    up common resources used in the project, such as hardware, software, protocols,
451    file formats and annotation types. In this case the power user is also responsible for
452    managing the LIMS.
453  </p>
454 
455  <ol>
456  <li>
457    Create a project:
458   
459    <table class="listing" cellspacing="0" cellpadding="2" border="0">
460    <tr>
461      <th>Name</th>
462      <th>Members</th>
463    </tr>
464    <tr>
465      <td>Project A</td>
466      <td>Groups: Group A (Use permission)</td>
467    </tr>
468    </table>
469    <p>
470  </li>
471 
472  <li>Activate the project.<p></li>
473 
474  <li>
475    Create protocols:
476    <table class="listing" cellspacing="0" cellpadding="2" border="0">
477    <tr>
478      <th>Name</th>
479      <th>Type</th>
480    </tr>
481    <tr>
482      <td>Sampling A</td>
483      <td>Sampling</td>
484    </tr>
485    <tr>
486      <td>Extraction A</td>
487      <td>Extraction</td>
488    </tr>
489    <tr>
490      <td>Labeling A</td>
491      <td>Labeling</td>
492    </tr>
493    <tr>
494      <td>Hybridization A</td>
495      <td>Hybridization</td>
496    </tr>
497    <tr>
498      <td>Scanning A</td>
499      <td>Scanning</td>
500    </tr>
501    <tr>
502      <td>Feature extraction A</td>
503      <td>Feature extraction</td>
504    </tr>
505    <tr>
506      <td>Printing A</td>
507      <td>Printing</td>
508    </tr>
509    </table>
510    <p>
511  </li>
512
513  <li>
514    Create hardware:
515    <table class="listing" cellspacing="0" cellpadding="2" border="0">
516    <tr>
517      <th>Name</th>
518      <th>Type</th>
519    </tr>
520    <tr>
521      <td>Hybridization station A</td>
522      <td>Hybridization station</td>
523    </tr>
524    <tr>
525      <td>Scanner A</td>
526      <td>Scanner</td>
527    </tr>
528    <tr>
529      <td>Print robot A</td>
530      <td>Print robot</td>
531    </tr>
532    </table>
533    <p>
534  </li>
535 
536  <li>
537    Create software:
538    <table class="listing" cellspacing="0" cellpadding="2" border="0">
539    <tr>
540      <th>Name</th>
541      <th>Type</th>
542    </tr>
543    <tr>
544      <td>Software A</td>
545      <td>Feature extraction</td>
546    </tr>
547    </table>
548    <p>
549  </li>
550 
551  <li>
552    Create annotation types:
553    <table class="listing" cellspacing="0" cellpadding="2" border="0">
554    <tr>
555      <th>Name</th>
556      <th>Type</th>
557      <th>Unit</th>
558      <th>Interface</th>
559      <th>Values</th>
560      <th>Item types</th>
561    </tr>
562    <tr>
563      <td>Drug resistance</td>
564      <td>String</td>
565      <td>-</td>
566      <td>radiobuttons</td>
567      <td>high, medium, low</td>
568      <td>Biosource</td>
569    </tr>
570    <tr>
571      <td>Time</td>
572      <td>Integer</td>
573      <td>Hour</td>
574      <td>text box</td>
575      <td>-</td>
576      <td>Sample</td>
577    </tr>
578    <tr>
579      <td>Dye swap</td>
580      <td>Boolean</td>
581      <td>-</td>
582      <td>-</td>
583      <td>-</td>
584      <td>Raw bioassay</td>
585    </tr>
586    </table>
587    <p>
588   
589  <li>
590    Create file formats (<i>i.e.</i>, plug-in configurations). The formats marked as
591    optional are not used in the test procedure, but may be useful to weed
592    out import problems, since they allow importing all info from the raw
593    data files. You may either enter the regular expressions as specified or
594    use the "Test with file" feature.
595   
596    <table class="listing" cellspacing="0" cellpadding="2" border="0">
597    <tr>
598      <th>Name</th>
599      <th>Plugin</th>
600      <th>Configuration values</th>
601    </tr>
602   
603    <tr class="oddrow">
604      <td>Plates for project A</td>
605      <td>Plate importer</td>
606      <td>
607     
608      <b>Test with file:</b> <code>plates_and_reporters.mouse.v4.37k.txt</code>
609      <table border="0" cellspacing="0" cellpadding="2">
610      <tr>
611        <td><i>Data header</i></td>
612        <td>384_number\t384_column\t384_row\t384_position\toligo_id.*</td>
613      </tr>
614      <tr>
615        <td><i>Data splitter</i></td>
616        <td>\t</td>
617      </tr>
618      <tr>
619        <td><i>Min data columns</i></td>
620        <td>5</td>
621      </tr>
622      <tr>
623        <td><i>Plate number/name</i></td>
624        <td>\384_number\</td>
625      </tr>
626      <tr>
627        <td><i>Row</i></td>
628        <td>\384_row\</td>
629      </tr>
630      <tr>
631        <td><i>Column</i></td>
632        <td>\384_column\</td>
633      </tr>
634      <tr>
635        <td><i>Reporter ID</i></td>
636        <td>\oligo_id\</td>
637      </tr>
638      </table>
639
640      </td>
641    </tr>
642   
643    <tr class="evenrow">
644      <td>GenePix feature importer<br>(optional)</td>
645      <td>Reporter map importer</td>
646      <td>
647     
648      <b>Test with file:</b> <code>genepix.mouse.v4.37k.00h.gpr</code>
649      <table border="0" cellspacing="0" cellpadding="2">
650      <tr>
651        <td><i>Data header</i></td>
652        <td>"Block"\t"Column"\t"Row"\t"Name"\t"ID"\t.*</td>
653      </tr>
654      <tr>
655        <td><i>Data splitter</i></td>
656        <td>\t</td>
657      </tr>
658      <tr>
659        <td><i>Min data columns</i></td>
660        <td>48</td>
661      </tr>
662      <tr>
663        <td><i>Max data columns</i></td>
664        <td>48</td>
665      </tr>
666      <tr>
667        <td><i>Reporter ID</i></td>
668        <td>\ID\</td>
669      </tr>
670      <tr>
671        <td><i>Block</i></td>
672        <td>\Block\</td>
673      </tr>
674      <tr>
675        <td><i>Column</i></td>
676        <td>\Column\</td>
677      </tr>
678      <tr>
679        <td><i>Row</i></td>
680        <td>\Row\</td>
681      </tr>
682      </table>
683
684      </td>
685    </tr>
686   
687    <tr class="oddrow">
688      <td>Raw data for project A</td>
689      <td>Raw data importer</td>
690      <td>
691     
692      <b>Test with file:</b> <code>genepix.mouse.v4.37k.00h.gpr</code>
693      <table border="0" cellspacing="0" cellpadding="2">
694      <tr>
695        <td><i>Raw data type</i></td>
696        <td>Genepix</td>
697      </tr>
698      <tr>
699        <td><i>Header</i></td>
700        <td>"(.+)=(.*)"</td>
701      </tr>
702      <tr>
703        <td><i>Data header</i></td>
704        <td>"Block"\t"Column"\t"Row"\t"Name"\t"ID"\t.*"Ratio of Medians \(532\/635\)".*</td>
705      </tr>
706      <tr>
707        <td><i>Data splitter</i></td>
708        <td>\t</td>
709      </tr>
710      <tr>
711        <td><i>Min data columns</i></td>
712        <td>48</td>
713      </tr>
714      <tr>
715        <td><i>Max data columns</i></td>
716        <td>48</td>
717      </tr>
718
719      <tr>
720        <td><i>Block</i></td>
721        <td>\Block\</td>
722      </tr>
723      <tr>
724        <td><i>Column</i></td>
725        <td>\Column\</td>
726      </tr>
727      <tr>
728        <td><i>Row</i></td>
729        <td>\Row\</td>
730      </tr>
731      <tr>
732        <td><i>X</i></td>
733        <td>\X\</td>
734      </tr>
735      <tr>
736        <td><i>Y</i></td>
737        <td>\Y\</td>
738      </tr>
739      <tr>
740        <td><i>Reporter ID</i></td>
741        <td>\ID\</td>
742      </tr>
743      <tr>
744        <td><i>Spot diameter</i></td>
745        <td>\Dia.\</td>
746      </tr>
747      <tr>
748        <td><i>Channel 1 foreground median</i></td>
749        <td>\F635 Median\</td>
750      </tr>
751      <tr>
752        <td><i>Channel 1 foreground mean</i></td>
753        <td>\F635 Mean\</td>
754      </tr>
755      <tr>
756        <td><i>Channel 1 foreground standard deviation</i></td>
757        <td>\F635 SD\</td>
758      </tr>
759      <tr>
760        <td><i>Channel 1 background median</i></td>
761        <td>\B635 Median\</td>
762      </tr>
763      <tr>
764        <td><i>Channel 1 background mean</i></td>
765        <td>\B635 Mean\</td>
766      </tr>
767      <tr>
768        <td><i>Channel 1 background standard deviation</i></td>
769        <td>\B635 SD\</td>
770      </tr>
771      <tr>
772        <td><i>Percent pixels within 1 standard deviation</i></td>
773        <td>\% > B635+1SD\</td>
774      </tr>
775      <tr>
776        <td><i>Percent pixels within 2 standard deviations</i></td>
777        <td>\% > B635+2SD\</td>
778      </tr>
779      <tr>
780        <td><i>Percent saturated pixels</i></td>
781        <td>\F635 % Sat.\</td>
782      </tr>
783      <tr>
784        <td><i>Channel 2 foreground median</i></td>
785        <td>\F532 Median\</td>
786      </tr>
787      <tr>
788        <td><i>Channel 2 foreground mean</i></td>
789        <td>\F532 Mean\</td>
790      </tr>
791      <tr>
792        <td><i>Channel 2 foreground standard deviation</i></td>
793        <td>\F532 SD\</td>
794      </tr>
795      <tr>
796        <td><i>Channel 2 background median</i></td>
797        <td>\B532 Median\</td>
798      </tr>
799      <tr>
800        <td><i>Channel 2 background mean</i></td>
801        <td>\B532 Mean\</td>
802      </tr>
803      <tr>
804        <td><i>Channel 2 background standard deviation</i></td>
805        <td>\B532 SD\</td>
806      </tr>
807      <tr>
808        <td><i>Percent pixels within 1 standard deviation</i></td>
809        <td>\% > B532+1SD\</td>
810      </tr>
811      <tr>
812        <td><i>Percent pixels within 2 standard deviations</i></td>
813        <td>\% > B532+2SD\</td>
814      </tr>
815      <tr>
816        <td><i>Percent saturated pixels</i></td>
817        <td>\F532 % Sat.\</td>
818      </tr>
819      <tr>
820        <td><i>Foreground pixels</i></td>
821        <td>\F Pixels\</td>
822      </tr>
823      <tr>
824        <td><i>Background pixels</i></td>
825        <td>\B Pixels\</td>
826      </tr>
827      <tr>
828        <td><i>Flags</i></td>
829        <td>\Flags\</td>
830      </tr>
831      </table>
832
833      </td>
834    </tr>
835   
836    <tr class="evenrow">
837      <td>Raw data for project A (dye-swap)</td>
838      <td>Raw data importer</td>
839      <td>
840
841      <b>Test with file:</b> <code>genepix.mouse.v4.37k.00h.dyeswap.gpr</code>
842      <table border="0" cellspacing="0" cellpadding="2">
843      <tr>
844        <td><i>Raw data type</i></td>
845        <td>Genepix</td>
846      </tr>
847      <tr>
848        <td><i>Header</i></td>
849        <td>"(.+)=(.*)"</td>
850      </tr>
851      <tr>
852        <td><i>Data header</i></td>
853        <td>"Block"\t"Column"\t"Row"\t"Name"\t"ID"\t.*"Ratio of Medians \(635\/532\)".*</td>
854      </tr>
855      <tr>
856        <td><i>Data splitter</i></td>
857        <td>\t</td>
858      </tr>
859      <tr>
860        <td><i>Min data columns</i></td>
861        <td>48</td>
862      </tr>
863      <tr>
864        <td><i>Max data columns</i></td>
865        <td>48</td>
866      </tr>
867
868      <tr>
869        <td><i>Block</i></td>
870        <td>\Block\</td>
871      </tr>
872      <tr>
873        <td><i>Column</i></td>
874        <td>\Column\</td>
875      </tr>
876      <tr>
877        <td><i>Row</i></td>
878        <td>\Row\</td>
879      </tr>
880      <tr>
881        <td><i>X</i></td>
882        <td>\X\</td>
883      </tr>
884      <tr>
885        <td><i>Y</i></td>
886        <td>\Y\</td>
887      </tr>
888      <tr>
889        <td><i>Reporter ID</i></td>
890        <td>\ID\</td>
891      </tr>
892      <tr>
893        <td><i>Spot diameter</i></td>
894        <td>\Dia.\</td>
895      </tr>
896      <tr>
897        <td><i>Channel 1 foreground median</i></td>
898        <td>\F532 Median\</td>
899      </tr>
900      <tr>
901        <td><i>Channel 1 foreground mean</i></td>
902        <td>\F532 Mean\</td>
903      </tr>
904      <tr>
905        <td><i>Channel 1 foreground standard deviation</i></td>
906        <td>\F532 SD\</td>
907      </tr>
908      <tr>
909        <td><i>Channel 1 background median</i></td>
910        <td>\B532 Median\</td>
911      </tr>
912      <tr>
913        <td><i>Channel 1 background mean</i></td>
914        <td>\B532 Mean\</td>
915      </tr>
916      <tr>
917        <td><i>Channel 1 background standard deviation</i></td>
918        <td>\B532 SD\</td>
919      </tr>
920      <tr>
921        <td><i>Percent pixels within 1 standard deviation</i></td>
922        <td>\% > B532+1SD\</td>
923      </tr>
924      <tr>
925        <td><i>Percent pixels within 2 standard deviations</i></td>
926        <td>\% > B532+2SD\</td>
927      </tr>
928      <tr>
929        <td><i>Percent saturated pixels</i></td>
930        <td>\F532 % Sat.\</td>
931      </tr>
932      <tr>
933        <td><i>Channel 2 foreground median</i></td>
934        <td>\F635 Median\</td>
935      </tr>
936      <tr>
937        <td><i>Channel 2 foreground mean</i></td>
938        <td>\F635 Mean\</td>
939      </tr>
940      <tr>
941        <td><i>Channel 2 foreground standard deviation</i></td>
942        <td>\F635 SD\</td>
943      </tr>
944      <tr>
945        <td><i>Channel 2 background median</i></td>
946        <td>\B635 Median\</td>
947      </tr>
948      <tr>
949        <td><i>Channel 2 background mean</i></td>
950        <td>\B635 Mean\</td>
951      </tr>
952      <tr>
953        <td><i>Channel 2 background standard deviation</i></td>
954        <td>\B635 SD\</td>
955      </tr>
956      <tr>
957        <td><i>Percent pixels within 1 standard deviation</i></td>
958        <td>\% > B635+1SD\</td>
959      </tr>
960      <tr>
961        <td><i>Percent pixels within 2 standard deviations</i></td>
962        <td>\% > B635+2SD\</td>
963      </tr>
964      <tr>
965        <td><i>Percent saturated pixels</i></td>
966        <td>\F635 % Sat.\</td>
967      </tr>
968      <tr>
969        <td><i>Foreground pixels</i></td>
970        <td>\F Pixels\</td>
971      </tr>
972      <tr>
973        <td><i>Background pixels</i></td>
974        <td>\B Pixels\</td>
975      </tr>
976      <tr>
977        <td><i>Flags</i></td>
978        <td>\Flags\</td>
979      </tr>
980      </table>
981
982      </td>
983    </tr>
984    </table>
985    <p>
986  </li>
987 
988  <li>
989    Annotate the file formats:
990    <table class="listing" cellspacing="0" cellpadding="2" border="0">
991    <tr>
992      <th>File format</th>
993      <th>Annotation</th>
994      <th>Value</th>
995    </tr>
996    <tr>
997      <td>Raw data for project A</td>
998      <td>Dye swap</td>
999      <td>false</td>
1000    </tr>
1001    <tr>
1002      <td>Raw data for project A (dye swap)</td>
1003      <td>Dye swap</td>
1004      <td>true</td>
1005    </tr>
1006    </table>
1007    This will make the raw data importer automatically annotate the
1008    raw bioassays with the specified annotations.
1009    <p>
1010  </li>
1011 
1012  <li>
1013    Create plate type:
1014    <table class="listing" cellspacing="0" cellpadding="2" border="0">
1015    <tr>
1016      <th>Name</th>
1017      <th>Geometry</th>
1018    </tr>
1019    <tr>
1020      <td>Plate type A</td>
1021      <td>384-well (16 x 24)</td>
1022    </tr>
1023    </table>
1024    <p>
1025  </li>
1026 
1027  <li>
1028    Import plates:
1029    <ol>
1030    <li>Go to the <code>Array LIMS -> Plates</code> page.</li>
1031    <li>Click on the <code>Import</code> button.</li>
1032    <li>Choose <code>auto-detect</code> and select
1033      the file <code>plates_and_reporters.mouse.v4.37k.txt</code>.</li>
1034    <li>The <code>Plates for project A</code> format should be
1035      found.</li>
1036    <li>Specify the following parameters:
1037   
1038      <table border="0" cellspacing="0" cellpadding="2">
1039      <tr>
1040        <td><i>Plate type</i></td>
1041        <td>Plate type A</td>
1042      </tr>
1043      <tr>
1044        <td><i>Plate name prefix</i></td>
1045        <td>Plate A</td>
1046      </tr>
1047      <tr>
1048        <td><i>Plate name padding</i></td>
1049        <td>4</td>
1050      </tr>
1051      </table>
1052    </li>
1053    <li>Continue and wait for the import to finish. It should create 96 plates.</li>
1054    </ol>
1055    <p>
1056  </li>
1057
1058  <li>
1059    Create array designs and upload data files to them:
1060    <table class="listing" cellspacing="0" cellpadding="2" border="0">
1061    <tr>
1062      <th>Name</th>
1063      <th>Platform</th>
1064      <th>File(s)</th>
1065    </tr>
1066    <tr>
1067      <td>Array design A</td>
1068      <td>Generic</td>
1069      <td><i>Print map</i>: printmap.mouse.v4.37k.tam</td>
1070    </tr>
1071    <tr>
1072      <td>Affymetrix A</td>
1073      <td>Affymetrix</td>
1074      <td><i>CDF file</i>: MG_U74Av2.cdf.bz2</td>
1075    </tr>
1076    </table>
1077    <p>
1078  </li>
1079 
1080  <li>
1081    Connect <code>Array design A</code> with plates. Select the imported plates (plate names starting
1082    with <code>Plate A</code>) and sort them in the correct order (as indicated by their names).
1083    <p>
1084  </li>
1085 
1086  <li>
1087    Import features:
1088    <ol>
1089    <li>Click on the <code>Import</code> button when viewing properties for the array design.</li>
1090    <li>Choose <code>auto-detect</code> and upload the file
1091      <code>printmap.mouse.v4.37k.tam</code>.</li>
1092    <li>The <code>Print map importer</code> plug-in should be
1093      found.</li>
1094    <li>Continue and wait for the import to finish. It should create 36,864 features and 48 blocks.</li>
1095    </ol>
1096    <p>
1097  </li>
1098
1099  <li>
1100    Set project defaults. Go to the projects page and edit the
1101    <code>Project A</code> project. On the <code>Defaults</code>
1102    tab, set the following defaults:
1103   
1104    <table class="listing" cellspacing="0" cellpadding="2" border="0">
1105    <tr>
1106      <th>Setting</th>
1107      <th>Value</th>
1108    </tr>
1109    <tr>
1110      <td>Platform / raw data type</td>
1111      <td>Generic / Genepix</td>
1112    </tr>
1113    <tr>
1114      <td>Software</td>
1115      <td>Software A</td>
1116    </tr>
1117    <tr>
1118      <td>Array design</td>
1119      <td>Array design A</td>
1120    </tr>
1121    <tr>
1122      <td>Hybridization station</td>
1123      <td>Hybridization station A</td>
1124    </tr>
1125    <tr>
1126      <td>Scanner</td>
1127      <td>Scanner A</td>
1128    </tr>
1129    <tr>
1130      <td>Print robot</td>
1131      <td>Print robot A</td>
1132    </tr>
1133    <tr>
1134      <td>Scanning protocol</td>
1135      <td>Scanning A</td>
1136    </tr>
1137    <tr>
1138      <td>Sampling protocol</td>
1139      <td>Sampling A</td>
1140    </tr>
1141    <tr>
1142      <td>Extraction protocol</td>
1143      <td>Extraction A</td>
1144    </tr>
1145    <tr>
1146      <td>Labeling protocol</td>
1147      <td>Labeling A</td>
1148    </tr>
1149    <tr>
1150      <td>Hybridization protocol</td>
1151      <td>Hybridization A</td>
1152    </tr>
1153    <tr>
1154      <td>Feat. extraction protocol</td>
1155      <td>Feature extraction A</td>
1156    </tr>
1157    <tr>
1158      <td>Printing protocol</td>
1159      <td>Printing A</td>
1160    </tr>
1161    </table>
1162   
1163    <p>
1164  </li>
1165
1166  <li>
1167    Create array batches:
1168    <table class="listing" cellspacing="0" cellpadding="2" border="0">
1169    <tr>
1170      <th>Name</th>
1171      <th>Array design</th>
1172      <th>Print robot</th>
1173      <th>Protocol</th>
1174    </tr>
1175    <tr>
1176      <td>Array batch A</td>
1177      <td>Array design A</td>
1178      <td>Robot A</td>
1179      <td>Printing A</td>
1180    </tr>
1181    <tr>
1182      <td>Affymetrix batch A</td>
1183      <td>Affymetrix A</td>
1184      <td></td>
1185      <td></td>
1186    </tr>
1187    </table>
1188    <p>
1189  </li>
1190
1191  <li>
1192    Create array slides with the <code>Create slides</code>
1193    wizard.
1194   
1195    <table class="listing" cellspacing="0" cellpadding="2" border="0">
1196    <tr>
1197      <th>Name</th>
1198      <th>Array batch</th>
1199      <th>Quantity</th>
1200    </tr>
1201    <tr>
1202      <td>Array slide A.</td>
1203      <td>Array batch A</td>
1204      <td>4</td>
1205    </tr>
1206    <tr>
1207      <td>Affymetrix slide A.</td>
1208      <td>Affymetrix batch A</td>
1209      <td>3</td>
1210    </tr>
1211    </table>
1212    <p>
1213  </li>
1214  </ol>
1215
1216  <a name="user"></a>
1217  <h2>5. User tests</h2>
1218  <p>
1219    The user is a typical worker in the project. The user does the actual experimentation in the
1220    lab, which includes collecting samples, doing extraction, labeling and hybridizations.
1221    The user also scans and analyses the raw data resulting from the images.
1222  </p>
1223 
1224  <ol>
1225  <li>
1226    Activate the <code>Project A</code> project<p></li>
1227   
1228  <li>
1229    Create a biosource:
1230    <table class="listing" cellspacing="0" cellpadding="2" border="0">
1231    <tr>
1232      <th>Name</th>
1233      <th>Annotations</th>
1234    </tr>
1235    <tr>
1236      <td>Biosource A</td>
1237      <td>
1238        <table border="0" cellspacing="0" cellpadding="2">
1239        <tr>
1240          <td><i>Drug resistance:</i></td>
1241          <td>medium</td>
1242        </tr>
1243        </table>
1244      </td>
1245    </tr>
1246    </table>
1247    <p>
1248  </li>
1249 
1250  <li>
1251    Create samples:
1252    <table class="listing" cellspacing="0" cellpadding="2" border="0">
1253    <tr>
1254      <th>Name</th>
1255      <th>Protocol</th>
1256      <th>Biosource</th>
1257      <th>Annotations</th>
1258    </tr>
1259    <tr>
1260      <td>Sample A.00h</td>
1261      <td>Sampling A</td>
1262      <td>Biosource A</td>
1263      <td>
1264        <table border="0" cellspacing="0" cellpadding="2">
1265        <tr>
1266          <td><i>Time (hours):</i></td>
1267          <td>0</td>
1268        </tr>
1269        </table>
1270      </td>
1271    </tr>
1272    <tr>
1273      <td>Sample A.24h</td>
1274      <td>Sampling A</td>
1275      <td>Biosource A</td>
1276      <td>
1277        <table border="0" cellspacing="0" cellpadding="2">
1278        <tr>
1279          <td><i>Time (hours):</i></td>
1280          <td>24</td>
1281        </tr>
1282        </table>
1283      </td>
1284    </tr>
1285    <tr>
1286      <td>Sample A.ref</td>
1287      <td>Sampling A</td>
1288      <td>-</td>
1289      <td>-</td>
1290    </tr>
1291    </table>
1292    <p>
1293  </li>
1294
1295  <li>
1296    Create extracts:
1297    <table class="listing" cellspacing="0" cellpadding="2" border="0">
1298    <tr>
1299      <th>Name</th>
1300      <th>Protocol</th>
1301      <th>Sample</th>
1302    </tr>
1303    <tr>
1304      <td>Extract A.00h</td>
1305      <td>Extraction A</td>
1306      <td>Sample A.00h</td>
1307    </tr>
1308    <tr>
1309      <td>Extract A.24h</td>
1310      <td>Extraction A</td>
1311      <td>Sample A.24h</td>
1312    </tr>
1313    <tr>
1314      <td>Extract A.ref</td>
1315      <td>Extraction A</td>
1316      <td>Sample A.ref</td>
1317    </tr>
1318    </table>
1319    <p>
1320  </li>
1321
1322  <li>
1323    Create labeled extracts:
1324    <table class="listing" cellspacing="0" cellpadding="2" border="0">
1325    <tr>
1326      <th>Name</th>
1327      <th>Label</th>
1328      <th>Protocol</th>
1329      <th>Extract</th>
1330    </tr>
1331    <tr>
1332      <td>Labeled extract A.00h</td>
1333      <td>cy3</td>
1334      <td>Labeling A</td>
1335      <td>Extract A.00h</td>
1336    </tr>
1337    <tr>
1338      <td>Labeled extract A.24h</td>
1339      <td>cy3</td>
1340      <td>Labeling A</td>
1341      <td>Extract A.24h</td>
1342    </tr>
1343    <tr>
1344      <td>Labeled extract A.ref</td>
1345      <td>cy5</td>
1346      <td>Labeling A</td>
1347      <td>Extract A.ref</td>
1348    </tr>
1349    <tr class="shaded">
1350      <td>Labeled extract A.00h (dye-swap)</td>
1351      <td>cy5</td>
1352      <td>Labeling A</td>
1353      <td>Extract A.00h</td>
1354    </tr>
1355    <tr class="shaded">
1356      <td>Labeled extract A.24h (dye-swap)</td>
1357      <td>cy5</td>
1358      <td>Labeling A</td>
1359      <td>Extract A.24h</td>
1360    </tr>
1361    <tr class="shaded">
1362      <td>Labeled extract A.ref (dye-swap)</td>
1363      <td>cy3</td>
1364      <td>Labeling A</td>
1365      <td>Extract A.ref</td>
1366    </tr>
1367    </table>
1368    <p>
1369  </li>
1370
1371  <li>
1372    Create hybridizations:
1373    <table class="listing" cellspacing="0" cellpadding="2" border="0">
1374    <tr>
1375      <th>Name</th>
1376      <th>Protocol</th>
1377      <th>Hardware</th>
1378      <th>Array slide</th>
1379      <th>Labeled extracts</th>
1380    </tr>
1381    <tr>
1382      <td>Hybridization A.00h</td>
1383      <td>Hybridization A</td>
1384      <td>Hybridization station A</td>
1385      <td>Array slide A.1</td>
1386      <td>Labeled extract A.00h,<br>Labeled extract A.ref</td>
1387    </tr>
1388    <tr>
1389      <td>Hybridization A.24h</td>
1390      <td>Hybridization A</td>
1391      <td>Hybridization station A</td>
1392      <td>Array slide A.2</td>
1393      <td>Labeled extract A.24h,<br>Labeled extract A.ref</td>
1394    </tr>
1395    <tr class="shaded">
1396      <td>Hybridization A.00h (dye-swap)</td>
1397      <td>Hybridization A</td>
1398      <td>Hybridization station A</td>
1399      <td>Array slide A.3</td>
1400      <td>Labeled extract A.00h (dye-swap),<br>Labeled extract A.ref (dye-swap)</td>
1401    </tr>
1402    <tr class="shaded">
1403      <td>Hybridization A.24h (dye-swap)</td>
1404      <td>Hybridization A</td>
1405      <td>Hybridization station A</td>
1406      <td>Array slide A.4</td>
1407      <td>Labeled extract A.24h (dye-swap),<br>Labeled extract A.ref (dye-swap)</td>
1408    </tr>
1409    <tr>
1410      <td>Affymetrix hyb A.1</td>
1411      <td>Hybridization A</td>
1412      <td>Hybridization station A</td>
1413      <td>Affymetrix slide A.1</td>
1414      <td>Labeled extract A.00h</td>
1415    </tr>
1416    <tr>
1417      <td>Affymetrix hyb A.2</td>
1418      <td>Hybridization A</td>
1419      <td>Hybridization station A</td>
1420      <td>Affymetrix slide A.2</td>
1421      <td>Labeled extract A.24h</td>
1422    </tr>
1423    <tr>
1424      <td>Affymetrix hyb A.3</td>
1425      <td>Hybridization A</td>
1426      <td>Hybridization station A</td>
1427      <td>Affymetrix slide A.3</td>
1428      <td>Labeled extract A.ref</td>
1429    </tr>
1430    </table>
1431    <p>
1432  </li>
1433 
1434  <li>
1435    Create scans:
1436    <table class="listing" cellspacing="0" cellpadding="2" border="0">
1437    <tr>
1438      <th>Name</th>
1439      <th>Hybridization</th>
1440      <th>Scanner</th>
1441      <th>Protocol</th>
1442    </tr>
1443    <tr>
1444      <td>Scan A.00h</td>
1445      <td>Hybridization A.00h</td>
1446      <td>Scanner A</td>
1447      <td>Scanning A</td>
1448    </tr>
1449    <tr>
1450      <td>Scan A.24h</td>
1451      <td>Hybridization A.24h</td>
1452      <td>Scanner A</td>
1453      <td>Scanning A</td>
1454    </tr>
1455    <tr class="shaded">
1456      <td>Scan A.00h (dye-swap)</td>
1457      <td>Hybridization A.00h (dye-swap)</td>
1458      <td>Scanner A</td>
1459      <td>Scanning A</td>
1460    </tr>
1461    <tr class="shaded">
1462      <td>Scan A.24h (dye-swap)</td>
1463      <td>Hybridization A.24h (dye-swap)</td>
1464      <td>Scanner A</td>
1465      <td>Scanning A</td>
1466    </tr>
1467    <tr>
1468      <td>Affymetrix scan A.1</td>
1469      <td>Affymetrix hyb A.1</td>
1470      <td>Scanner A</td>
1471      <td>Scanning A</td>
1472    </tr>
1473    <tr>
1474      <td>Affymetrix scan A.2</td>
1475      <td>Affymetrix hyb A.2</td>
1476      <td>Scanner A</td>
1477      <td>Scanning A</td>
1478    </tr>
1479    <tr>
1480      <td>Affymetrix scan A.3</td>
1481      <td>Affymetrix hyb A.3</td>
1482      <td>Scanner A</td>
1483      <td>Scanning A</td>
1484    </tr>
1485    </table>
1486    <p>
1487  </li>
1488 
1489  <li>
1490    Add images to the scans (TODO - we don't have any images yet):
1491    <table class="listing" cellspacing="0" cellpadding="2" border="0">
1492    <tr>
1493      <th>Scan</th>
1494      <th>Image files</th>
1495    </tr>
1496    <tr>
1497      <td>Scan A.00h</td>
1498      <td>-</td>
1499    </tr>
1500    <tr>
1501      <td>Scan A.24h</td>
1502      <td>-</td>
1503    </tr>
1504    <tr class="shaded">
1505      <td>Scan A.00h (dye-swap)</td>
1506      <td>-</td>
1507    </tr>
1508    <tr class="shaded">
1509      <td>Scan A.24h (dye-swap)</td>
1510      <td>-</td>
1511    </tr>
1512    </table>
1513    <p>
1514  </li>
1515
1516  <li>
1517    Create raw bioassays:
1518    <table class="listing" cellspacing="0" cellpadding="2" border="0">
1519    <tr>
1520      <th>Name</th>
1521      <th>Platform/Raw data type</th>
1522      <th>Array design</th>
1523      <th>Protocol</th>
1524      <th>Scan</th>
1525      <th>Software</th>
1526      <th>File(s)</th>
1527    </tr>
1528    <tr>
1529      <td>Raw bioassay A.00h</td>
1530      <td>Generic/GenePix</td>
1531      <td>Array design A</td>
1532      <td>Feature extraction A</td>
1533      <td>Scan A.00h</td>
1534      <td>Software A</td>
1535      <td><i>Raw data</i>: genepix.mouse.v4.37k.00h.gpr</td>
1536    </tr>
1537    <tr>
1538      <td>Raw bioassay A.24h</td>
1539      <td>Generic/GenePix</td>
1540      <td>Array design A</td>
1541      <td>Feature extraction A</td>
1542      <td>Scan A.24h</td>
1543      <td>Software A</td>
1544      <td><i>Raw data</i>: genepix.mouse.v4.37k.24h.gpr</td>
1545    </tr>   
1546    <tr class="shaded">
1547      <td>Raw bioassay A.00h (dye-swap)</td>
1548      <td>Generic/GenePix</td>
1549      <td>Array design A</td>
1550      <td>Feature extraction A</td>
1551      <td>Scan A.00h (dye-swap)</td>
1552      <td>Software A</td>
1553      <td><i>Raw data</i>: genepix.mouse.v4.37k.00h.dyeswap.gpr</td>
1554    </tr> 
1555    <tr class="shaded">
1556      <td>Raw bioassay A.24h (dye-swap)</td>
1557      <td>Generic/GenePix</td>
1558      <td>Array design A</td>
1559      <td>Feature extraction A</td>
1560      <td>Scan A.24h (dye-swap)</td>
1561      <td>Software A</td>
1562      <td><i>Raw data</i>: genepix.mouse.v4.37k.24h.dyeswap.gpr</td>
1563    </tr>
1564    <tr>
1565      <td>Affymetrix raw A.1</td>
1566      <td>Affymetrix</td>
1567      <td>Affymetrix A</td>
1568      <td>Feature extraction A</td>
1569      <td>Affymetrix scan A.1</td>
1570      <td>Software A</td>
1571      <td><i>CEL file</i>: jos1761.cel.bz2</td>
1572    </tr>   
1573    <tr>
1574      <td>Affymetrix raw A.2</td>
1575      <td>Affymetrix</td>
1576      <td>Affymetrix A</td>
1577      <td>Feature extraction A</td>
1578      <td>Affymetrix scan A.2</td>
1579      <td>Software A</td>
1580      <td><i>CEL file</i>: jos1762.cel.bz2</td>
1581    </tr>   
1582    <tr>
1583      <td>Affymetrix raw A.3</td>
1584      <td>Affymetrix</td>
1585      <td>Affymetrix A</td>
1586      <td>Feature extraction A</td>
1587      <td>Affymetrix scan A.3</td>
1588      <td>Software A</td>
1589      <td><i>CEL file</i>: jos1763.cel.bz2</td>
1590    </tr>   
1591    </table>
1592    <p>
1593  </li>
1594 
1595  <li>
1596    Inherit the annotations from the samples and biosource for each raw bioassay.
1597    <p>
1598   
1599  </li>
1600 
1601  <li>
1602    Use the auto-detect feature to upload and import raw data for each
1603    Genepix raw bioassay. Select the <code>smart</code> option for the "Feature mismatch"
1604    parameter and <code>null</code> for "Invalid numeric value".
1605   
1606    <table class="listing" cellspacing="0" cellpadding="2" border="0">
1607    <tr>
1608      <th>Raw bioassay</th>
1609      <th>Raw data file</th>
1610      <th>Spots inserted/with null reporter/skipped)</th>
1611      <th>Annotations created</th>
1612    </tr>
1613    <tr>
1614      <td>Raw bioassay A.00h</td>
1615      <td>genepix.mouse.v4.37k.00h.gpr</td>
1616      <td>36,864/632/768</td>
1617      <td><i>Dye swap</i>: false</td>
1618    </tr>
1619    <tr>
1620      <td>Raw bioassay A.24h</td>
1621      <td>genepix.mouse.v4.37k.24h.gpr</td>
1622      <td>36,864/632/768</td>
1623      <td><i>Dye swap</i>: false</td>
1624    </tr>   
1625    <tr class="shaded">
1626      <td>Raw bioassay A.00h (dye-swap)</td>
1627      <td>genepix.mouse.v4.37k.00h.dyeswap.gpr</td>
1628      <td>36,864/632/768</td>
1629      <td><i>Dye swap</i>: true</td>
1630    </tr> 
1631    <tr class="shaded">
1632      <td>Raw bioassay A.24h (dye-swap)</td>
1633      <td>genepix.mouse.v4.37k.24h.dyeswap.gpr</td>
1634      <td>36,864/632/768</td>
1635      <td><i>Dye swap</i>: true</td>
1636    </tr>
1637    </table>
1638    <p>
1639  </li>
1640 
1641  <li>
1642    Create experiments:
1643    <table class="listing" cellspacing="0" cellpadding="2" border="0">
1644    <tr>
1645      <th>Name</th>
1646      <th>Raw data type</th>
1647      <th>Raw bioassays</th>
1648      <th>Experimental factors</th>
1649    </tr>
1650    <tr>
1651      <td>Experiment A</td>
1652      <td>GenePix</td>
1653      <td>Raw bioassay A.00h,<br>Raw bioassay A.24h,<br>Raw bioassay A.00h (dye-swap),<br>
1654        Raw bioassay A.24h (dye-swap)</td>
1655      <td>Drug resistance, Time (hours), Dye swap</td>
1656    </tr>
1657    <tr>
1658      <td>Affymetrix A</td>
1659      <td>Affymetrix</td>
1660      <td>Affymetrix raw A.1,<br>Affymetrix raw A.2,<br>Affymetrix raw A.3</td>
1661      <td>Drug resistance, Time (hours)</td>
1662    </tr>
1663    </table>
1664    <p>
1665  </li>
1666 
1667  <li>
1668    Check the experiment overview page. It should display one warnings for the
1669    Genepix experiment. The warning is related to a missing biosurce
1670    on the reference sample.
1671    <p>
1672    The Affymetrix experiment gives some more warnings. Most of them are
1673    related to not using the project default items, missing protocols
1674    and missing hardware. There should also be an error about missing
1675    experimental factor values for the <code>Affymetrix.3</code>
1676    raw bioassay. It is expected since this comes from the reference sample
1677    which doesn't have values for those annotations.
1678    <p>
1679   
1680    Change validation options to reduce the number of warnings:
1681    <table class="listing" cellspacing="0" cellpadding="2" border="0">
1682    <tr>
1683      <th>Validation option</th>
1684      <th>Setting</th>
1685    </tr>
1686    <tr>
1687      <td>Project defaults</td>
1688      <td>Set all to <code>Ignore</code></td>
1689    </tr>
1690    <tr>
1691      <td>Missing items</td>
1692      <td>Set all to <code>Ignore</code></td>
1693    </tr>
1694    <tr>
1695      <td>Annotations - Missing factor value</td>
1696      <td><code>Warning</code></td>
1697    </tr>
1698    </table>
1699   
1700    After the changes there should now only be two warnings about the
1701    missing factor values.
1702   
1703    <p>
1704  </li>
1705 
1706  </ol>
1707
1708  <a name="analysis"></a>
1709  <h2>6. Analysis tests</h2>
1710  <p>
1711    Now it is time to analyse the data. The analysis test should be done
1712    by both a regular user and a guest.
1713  </p>
1714 
1715  <ol>
1716  <li>
1717    Activate the <code>Project A</code> project<p>
1718  </li>
1719   
1720  <li>
1721    Go to the <code>Experiment A</code> experiment and select
1722    the <code>Bioassay sets</code> tab.
1723    <p>
1724  </li>
1725 
1726  <li>
1727    Create a new root bioassay set:
1728    <table class="listing" cellspacing="0" cellpadding="2" border="0">
1729    <tr>
1730      <th>Bioassay set name</th>
1731      <th>Raw bioassays</th>
1732      <th>Formula</th>
1733    </tr>
1734    <tr>
1735      <td>Root bioassay set</td>
1736      <td>all</td>
1737      <td>Mean FG - Mean BG</td>
1738    </tr>
1739    </table>
1740    Wait for the plug-in to finish.
1741    <p>
1742  </li>
1743 
1744  <li>
1745    Select the created bioassay set and create a filtered bioassayset:
1746    <table class="listing" cellspacing="0" cellpadding="2" border="0">
1747    <tr>
1748      <th>Child name</th>
1749      <th>Filter preset</th>
1750      <th>Expression</th>
1751    </tr>
1752    <tr>
1753      <td>Filtered bioassay set</td>
1754      <td>-</td>
1755      <td>ch(1) &gt; 0 &amp;&amp; ch(2) &gt; 0 &amp;&amp; rep('id') != null</td>
1756    </tr>
1757    </table>
1758    Wait for the plug-in to finish. It should report that 136,498 spots remain and
1759    that 10,958 spots has been removed.
1760    <p>
1761  </li>
1762
1763  <li>
1764    Select the filtered bioassay set and run a normalization plug-in:
1765    <table class="listing" cellspacing="0" cellpadding="2" border="0">
1766    <tr>
1767      <th>Plugin</th>
1768      <th>Parameters</th>
1769    </tr>
1770    <tr>
1771      <td>Normalization: Lowess</td>
1772      <td>Accept the most of default parameters, but change the
1773      "Block group size" to 12. Otherwise it will take too long time.</td>
1774    </tr>
1775    </table>
1776    Wait for the plug in to finish. It should report that 136,498 spots has been
1777    normalized and 0 spots has been removed.
1778    <p>
1779  </li>
1780   
1781  <li>
1782    Select the normalized bioassay set and check the overview plots and
1783    the correction factor plots. Here are four examples:
1784    <table class="listing" cellspacing="0" cellpadding="2" border="0">
1785    <tr>
1786      <th>Overview plots</th>
1787      <th>Correction factor plots</th>
1788    </tr>
1789    <tr>
1790      <td><img src="overview.png"><br><img src="overview.dyeswap.png"></td>
1791      <td><img src="correction.png"><br><img src="correction.dyeswap.png"></td>
1792    </tr>
1793    </table>
1794    <p>
1795  </li>
1796 
1797  <li>
1798    Try the plot tool with the following plots. Use the <code>Save</code> function
1799    to save one them as a file in the BASE file system, and the <code>Download</code> 
1800    function  to download a plot to your computer.
1801    <table class="listing" cellspacing="0" cellpadding="2" border="0">
1802    <tr>
1803      <th>Plot type</th>
1804      <th>Y-axis preset</th>
1805      <th>X-axis preset</th>
1806      <th>Other options</th>
1807    </tr>
1808    <tr>
1809      <td>Scatter plot</td>
1810      <td>M, log2(ch1 / ch2)</td>
1811      <td>A, log10(ch1 * ch2) / 2</td>
1812      <td>-</td>
1813    </tr>
1814    <tr>
1815      <td>Histogram plot</td>
1816      <td>Count</td>
1817      <td>Ratio, ch1 / ch2</td>
1818      <td>
1819        <table border="0" cellspacing="0" cellpadding="2">
1820        <tr>
1821          <td><i>Log scale</i></td>
1822          <td>checked</td>
1823        </tr>
1824        <tr>
1825          <td><i>Bin size</i></td>
1826          <td>0.1</td>
1827        </tr>
1828        <tr>
1829          <td><i>Annotation</i></td>
1830          <td>Time (hours)</td>
1831        </tr>
1832        </table>
1833      </td>
1834    </tr>
1835    </table>
1836    <p>
1837    Here are two examples:
1838    <table class="listing" cellspacing="0" cellpadding="2" border="0">
1839    <tr>
1840      <th>Scatter plot</th>
1841    </tr>
1842    <tr>
1843      <td><img src="scatter.png"></td>
1844    </tr>
1845    </table>
1846    <p>
1847    <table class="listing" cellspacing="0" cellpadding="2" border="0">
1848    <tr>
1849      <th>Histogram plot</th>
1850    </tr>
1851    <tr>
1852      <td><img src="histogram.png"></td>
1853    </tr>
1854    </table>
1855    <p>
1856  </li>
1857 
1858  </ol>
1859
1860
1861</body>
1862</html>
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