source: trunk/doc/test/roles/index.html @ 6958

Last change on this file since 6958 was 6958, checked in by Nicklas Nordborg, 6 years ago

References #1941: Store experimental factor values as part experiments

Updated test program to set experimental factor values on root raw bioassays instead of raw bioassays.

Noted that the "Item overview validation" now complains about missing experimental factors, probably because it has not been updated and still check the raw bioassays and not the root raw bioassays.

  • Property svn:eol-style set to native
  • Property svn:keywords set to Date Id
File size: 58.0 KB
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1<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
2<!--
3  $Id: index.html 6958 2015-09-30 12:55:14Z nicklas $
4
5  Copyright (C) 2006 Jari Häkkinen, 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="../../historical/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: 2015-09-30 12:55:14 +0000 (Wed, 30 Sep 2015) $
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>Array LIMS information - plate type, plates, array design, array batch and array slides</li>
111    <li>Biomaterial LIMS information - bioplate type</li>
112    </ul>
113  </li>
114 
115  <li>The user creates items related to an actual experiment:
116    <ul>
117    <li>Biomaterials: bioplate, biosources, samples, extracts, etc.</li>
118    <li>Experiment: physical bioassays, derived bioassays, raw bioassays</li>
119    <li>Import raw data</li>
120    </ul>
121  </li>
122 
123  <li>Both the user and the guest then do some analysis:
124    <ul>
125    <li>Create a root bioassay set</li>
126    <li>Filter the bioassay set</li>
127    <li>Run a normalization plug-in</li>
128    <li>Check the result by listing and plotting the data</li>
129    </ul>
130  </li>
131  </ol>
132
133  <p>
134    These tests can also be run in automated mode by test programs. This will of
135    course not test the web client, but are useful if one quickly needs to do
136    parts of the test and then continue with, for example, the user or analysis tests
137    on the web.
138  </p>
139 
140  <p>
141    The data files needed by the tests are NOT included in the subversion repository.
142    The main reason is that they are too large, and that we don't have permission to
143    make them publicly available for download. To get the test file you need to be a
144    core developer. Read the instructions on the
145    <a href="http://base.thep.lu.se/wiki/DeveloperInformation">DeveloperInformation</a>
146    page, <code>Test data</code> section on the BASE web site. The automated
147    test programs require that file are placed (checked out) in the 'testdata'
148    directory located in the BASE root directory. NOTE! Some test data files are
149    bzip-compressed. Use the automatic unpacking that is built-in to BASE when
150    uploading.
151  </p>
152 
153  <p>
154    To run the tests do the following:
155  </p>
156  <ol>
157   
158    <li>Compile the core and the test programs: <code>ant main test</code>.</li>
159
160    <li>Change to the <code>build/test/</code> directory.</li>
161
162    <li>Run test programs: <code>./test.sh roles [OPTION] &lt;cmds&gt;</code> where
163      <code>&lt;cmds&gt;</code> is one or more of the following:
164      <ul>
165      <li><code>all</code>: run all tests</li>
166      <li><code>root</code>: run the root user tests</li>
167      <li><code>admin</code>: run the administrator tests</li>
168      <li><code>power</code>: run the power user tests</li>
169      <li><code>user</code>: run the regular user tests</li>
170      <li><code>guest</code>: run the guest user tests</li>
171      </ul>
172      and <code>OPTION</code> can be none or more of:
173      <ul>
174      <li><code>-b</code>: if the batch importers should be tested</li>
175      </ul>
176    </li>
177   
178  </ol>
179   
180  <a name="root"></a>
181  <h2>2. Root user tests</h2>
182  <p>
183    The root user creates an administrator which is a server-wide admin.
184  </p>
185 
186  <ol>
187  <li>
188    Create a new user and set the following
189    properties. All other properties may remain unchanged.
190   
191    <table class="listing" cellspacing="0" cellpadding="2" border="0">
192    <tr>
193      <th>Name</th>
194      <th>Login/Password</th>
195      <th>Quota</th>
196      <th>Quota group</th>
197      <th>Membership</th>
198    </tr>
199    <tr>
200      <td>Admin</td>
201      <td>admin/admin</td>
202      <td>Unlimited</td>
203      <td>-</td>
204      <td>Roles: Administrator</td>
205    </tr>
206    </table>
207  </li>
208  </ol>
209
210  <a name="admin"></a>
211  <h2>3. Administrator tests</h2>
212  <p>
213    The administrator creates users for a project and gives them permissions
214    that are suitable for their role in the project. The administrator also
215    sets up quota and group membership.
216  </p>
217
218  <ol>
219  <li>
220    Create a new group and set the following properties:
221 
222    <table class="listing" cellspacing="0" cellpadding="2" border="0">
223    <tr>
224      <th>Name</th>
225      <th>Quota</th>
226    </tr>
227    <tr>
228      <td>Group A</td>
229      <td>1GB</td>
230    </tr>
231    </table>
232    <p>
233  </li>
234 
235  <li>
236    Create the following users:
237
238    <table class="listing" cellspacing="0" cellpadding="2" border="0">
239    <tr>
240      <th>Name</th>
241      <th>Login/Password</th>
242      <th>Quota</th>
243      <th>Quota group</th>
244      <th>Membership</th>
245      <th>Other</th>
246    </tr>
247    <tr>
248      <td>Power user</td>
249      <td>power/power</td>
250      <td>1GB</td>
251      <td>Group A</td>
252      <td>Roles: Power user</td>
253      <td>-</td>
254    </tr>
255    <tr>
256      <td>User</td>
257      <td>user/user</td>
258      <td>1GB</td>
259      <td>Group A</td>
260      <td>Roles: User</td>
261      <td>-</td>
262    </tr>
263    <tr>
264      <td>Guest</td>
265      <td>guest/guest</td>
266      <td>10MB</td>
267      <td>Group A</td>
268      <td>Roles: Guest</td>
269      <td><i>Multi-user account</i> checked</td>
270    </tr>
271    </table>
272    <p>
273  </li>
274 
275  <li>Give USE permission for the listed users to the following plugins:
276 
277    <table class="listing" cellspacing="0" cellpadding="2" border="0">
278    <tr>
279      <th>User</th>
280      <th>Plugins</th>
281    </tr>
282    <tr>
283      <td>Power user</td>
284      <td>
285        <ul>
286        <li>Plate importer</li>
287        <li>Reporter map importer</li>
288        <li>Print map importer</li>
289        <li>GTF reporter map importer</li>
290        <li>Array design importer</li>
291        <li>Array batch importer</li>
292        <li>Array slide importer</li>
293        </ul>
294      </td>
295    </tr>
296    </table>
297    <p>
298  </li>
299
300  <li>
301    Create file formats (<i>i.e.</i>, plug-in configurations) for importing
302    reporters. The formats marked as
303    optional are not used in the test procedure, but may be useful to weed
304    out import problems, since they allow importing all info from the raw
305    data files. You may either enter the regular expressions as specified or
306    use the "Test with file" feature.
307   
308    <table class="listing" cellspacing="0" cellpadding="2" border="0">
309    <tr>
310      <th>Name</th>
311      <th>Plugin</th>
312      <th>Configuration values</th>
313    </tr>
314    <tr class="oddrow">
315      <td>Reporters for project A</td>
316      <td>Reporter importer</td>
317      <td>
318      <table border="0" cellspacing="0" cellpadding="2">
319      <tr>
320        <td><b>File</b></td>
321        <td><code>mouse/<br>plates_and_reporters.mouse.v4.37k.txt</code></td>
322      </tr>
323      <tr>
324        <td><i>Data header</i></td>
325        <td>384_number\t384_column\t384_row\t384_position\toligo_id.*</td>
326      </tr>
327      <tr>
328        <td><i>Data splitter</i></td>
329        <td>\t</td>
330      </tr>
331      <tr>
332        <td><i>Min data columns</i></td>
333        <td>5</td>
334      </tr>
335      <tr>
336        <td><i>Name</i></td>
337        <td>\oligo_id\</td>
338      </tr>
339      <tr>
340        <td><i>External ID</i></td>
341        <td>\oligo_id\</td>
342      </tr>
343      <tr>
344        <td><i>Description</i></td>
345        <td>\description_Ensembl*\</td>
346      </tr>
347      <tr>
348        <td><i>Gene symbol</i></td>
349        <td>\gene_symbol_Ensembl*\</td>
350      </tr>
351      <tr>
352        <td><i>Sequence</i></td>
353        <td>\oligo_sequence\</td>
354      </tr>
355      </table>
356     
357      </td>
358    </tr>
359   
360    <tr class="evenrow">
361      <td>GenePix reporter importer<br>(optional)</td>
362      <td>Reporter importer</td>
363      <td>
364
365      <table border="0" cellspacing="0" cellpadding="2">
366      <tr>
367        <td><b>File</b></td>
368        <td><code>mouse/<br>genepix.mouse.v4.37k.00h.gpr</code></td>
369      </tr>
370      <tr>
371        <td><i>Data header</i></td>
372        <td>"Block"\t"Column"\t"Row"\t"Name"\t"ID"\t.*</td>
373      </tr>
374      <tr>
375        <td><i>Data splitter</i></td>
376        <td>\t</td>
377      </tr>
378      <tr>
379        <td><i>Min data columns</i></td>
380        <td>48</td>
381      </tr>
382      <tr>
383        <td><i>Max data columns</i></td>
384        <td>48</td>
385      </tr>
386      <tr>
387        <td><i>Name</i></td>
388        <td>\Name\</td>
389      </tr>
390      <tr>
391        <td><i>External ID</i></td>
392        <td>\ID\</td>
393      </tr>
394      </table>
395
396      </td>
397    </tr>
398    <tr class="oddrow">
399      <td>Reporters from Affymetrix annotations file</td>
400      <td>Reporter importer</td>
401      <td>
402      <table border="0" cellspacing="0" cellpadding="2">
403      <tr>
404        <td><b>File</b></td>
405        <td><code>affymetrix/annotations/<br>MG_U74Av2_annot.csv.bz2</code></td>
406      </tr>
407      <tr>
408        <td><i>Data header</i></td>
409        <td>"Probe Set ID","GeneChip Array".*</td>
410      </tr>
411      <tr>
412        <td><i>Data splitter</i></td>
413        <td>(?!"),(?=")</td>
414      </tr>
415      <tr>
416        <td><i>Name</i></td>
417        <td>\Probe Set ID\</td>
418      </tr>
419      <tr>
420        <td><i>External ID</i></td>
421        <td>\Probe Set ID\</td>
422      </tr>
423      <tr>
424        <td><i>Description</i></td>
425        <td>\Target Description\</td>
426      </tr>
427      <tr>
428        <td><i>Gene symbol</i></td>
429        <td>\Gene Symbol\</td>
430      </tr>
431      </table>
432     
433      </td>
434    </tr>   
435    <tr class="evenrow">
436      <td>Reporters from GTF file</td>
437      <td>GTF Reporter importer</td>
438      <td>
439
440      <table border="0" cellspacing="0" cellpadding="2">
441      <tr>
442        <td><b>File</b></td>
443        <td><code>sequencing/<br>UCSC_Human_hg19_RefSeqGenes.gtf.tar.bz2</code></td>
444      </tr>
445      <tr>
446        <td><i>Data header</i></td>
447        <td>&lt;seqname&gt;\t.*&lt;transcript_id&gt;.*</td>
448      </tr>
449      <tr>
450        <td><i>Data splitter</i></td>
451        <td>\t</td>
452      </tr>
453      <tr>
454        <td><i>Min data columns</i></td>
455        <td>4</td>
456      </tr>
457      <tr>
458        <td><i>Remove quotes</i></td>
459        <td>yes</td>
460      </tr>
461      <tr>
462        <td><i>Complex mappings</i></td>
463        <td>allow</td>
464      </tr>
465      <tr>
466        <td><i>Name</i></td>
467        <td>\&lt;transcript_id&gt;\@\&lt;seqname&gt;\</td>
468      </tr>
469      <tr>
470        <td><i>External ID</i></td>
471        <td>\&lt;transcript_id&gt;\@\&lt;seqname&gt;\</td>
472      </tr>
473      <tr>
474        <td><i>Gene symbol</i></td>
475        <td>\&lt;gene_id&gt;\</td>
476      </tr>
477      <tr>
478        <td><i>Chromosome</i></td>
479        <td>\&lt;seqname&gt;\</td>
480      </tr>
481      </table>
482
483      </td>
484    </tr>
485    </table>
486    <p>
487    </li>
488
489    <li>
490      Import reporters:
491      <ol>
492      <li>Go to the <code>View -> Reporters</code> page.</li>
493      <li>Click on the <code>Import</code> button.</li>
494      <li>Choose <code>auto-detect</code> and then upload
495        the file <code>plates_and_reporters.mouse.v4.37k.txt</code>.</li>
496      <li>The <code>Reporters for project A</code> format should be
497        found.</li>
498      <li>Select the <code>skip</code> option for the "Missing a required" value
499        since the file contains rows with empty reporter ID:s.
500      <li>Continue and wait for the import to finish. It should create 35,912 new reporters.</li>
501      <li>
502        Repeat the procedure with the <code>MG_U74Av2_annot.csv</code> file. This time
503        also select <code>crop</code> for the "String too long" setting since
504        the file contains data that is too large for the datbase.
505        12,488 new reporters should be created.
506      <li>
507        Repeat the procedure with the <code>UCSC_Human_hg19_RefSeqGenes.gtf</code> 
508        file. The default error handling options can be used. This time
509        38,977 new reporters should be created.
510      </ol>
511      <p>
512 
513    </li>
514
515
516  </ol>
517
518
519  <a name="power"></a>
520  <h2>4. Power user tests</h2>
521  <p>
522    The power user is the typical owner/administrator of a project. The power user sets
523    up common resources used in the project, such as hardware, software, protocols,
524    file formats and annotation types. In this case the power user is also responsible for
525    managing the LIMS.
526  </p>
527 
528  <ol>
529  <li>
530    Create a project:
531   
532    <table class="listing" cellspacing="0" cellpadding="2" border="0">
533    <tr>
534      <th>Name</th>
535      <th>Members</th>
536    </tr>
537    <tr>
538      <td>Project A</td>
539      <td>Groups: Group A (Use permission)</td>
540    </tr>
541    </table>
542    <p>
543  </li>
544 
545  <li>Activate the project.<p></li>
546 
547  <li>
548    Create annotation types [A] and protocol parameters [P]:
549    <table class="listing" cellspacing="0" cellpadding="2" border="0">
550    <tr>
551      <th>Name</th>
552      <th>Type</th>
553      <th>Unit</th>
554      <th>Interface</th>
555      <th>Values</th>
556      <th>Item types</th>
557    </tr>
558    <tr>
559      <td>Drug resistance [A]</td>
560      <td>String</td>
561      <td>-</td>
562      <td>radiobuttons</td>
563      <td>high, medium, low</td>
564      <td>Biosource</td>
565    </tr>
566    <tr>
567      <td>Time [A]</td>
568      <td>Integer</td>
569      <td>Hour</td>
570      <td>text box</td>
571      <td>-</td>
572      <td>Sample</td>
573    </tr>
574    <tr>
575      <td>RIN [A]</td>
576      <td>Float</td>
577      <td>-</td>
578      <td>text box</td>
579      <td>-</td>
580      <td>Extract</td>
581    </tr>
582    <tr>
583      <td>Dye swap [A]</td>
584      <td>Boolean</td>
585      <td>-</td>
586      <td>-</td>
587      <td>-</td>
588      <td>Raw bioassay</td>
589    </tr>
590    <tr>
591      <td>PMT gain [P]</td>
592      <td>Float</td>
593      <td>Volt (Electric potential)</td>
594      <td>-</td>
595      <td>-</td>
596      <td>Derived bioassay</td>
597    </tr>
598    </table>
599    <p>
600  </li>
601 
602  <li>
603    Create item subtypes:
604    <table class="listing" cellspacing="0" cellpadding="2" border="0">
605    <tr>
606      <th>Name</th>
607      <th>Item type</th>
608      <th>Push annotations to parent</th>
609    </tr>
610    <tr>
611      <td>Quality control</td>
612      <td>Extract</td>
613      <td>Yes</td>
614    </tr>
615    </table>
616    <p>
617  </li>
618 
619  <li>
620    Create protocols (keep the 'Add as project default' option checked and the 'Replace existing default' unchecked):
621    <table class="listing" cellspacing="0" cellpadding="2" border="0">
622    <tr>
623      <th>Name</th>
624      <th>Type</th>
625      <th>Comment</th>
626    </tr>
627    <tr>
628      <td>Sampling A</td>
629      <td>Sampling</td>
630    </tr>
631    <tr>
632      <td>Extraction A</td>
633      <td>Extraction</td>
634    </tr>
635    <tr>
636      <td>Labeling A</td>
637      <td>Labeling</td>
638    </tr>
639    <tr>
640      <td>Library preparation A</td>
641      <td>Library preparation</td>
642    </tr>
643    <tr>
644      <td>Hybridization A</td>
645      <td>Hybridization</td>
646    </tr>
647    <tr>
648      <td>cBot Settings A</td>
649      <td>Cluster generation</td>
650    </tr>
651    <tr>
652      <td>Scanning A</td>
653      <td>Scanning</td>
654      <td>Select 'PMT gain' as a protocol parameter.</td>
655    </tr>
656    <tr>
657      <td>HiSeq Settings A</td>
658      <td>Sequencing</td>
659    </tr>
660    <tr>
661      <td>TopHat Settings A</td>
662      <td>Alignment</td>
663    </tr>
664    <tr>
665      <td>Feature extraction A</td>
666      <td>Feature extraction</td>
667    </tr>
668    <tr>
669      <td>Cufflinks Settings A</td>
670      <td>Feature extraction</td>
671    </tr>
672    <tr>
673      <td>Printing A</td>
674      <td>Printing</td>
675    </tr>
676    </table>
677    <p>
678  </li>
679
680  <li>
681    Create hardware (keep the 'Add as project default' option checked and the 'Replace existing default' unchecked):
682    <table class="listing" cellspacing="0" cellpadding="2" border="0">
683    <tr>
684      <th>Name</th>
685      <th>Type</th>
686    </tr>
687    <tr>
688      <td>Hybridization station A</td>
689      <td>Hybridization station</td>
690    </tr>
691    <tr>
692      <td>cBot A</td>
693      <td>Cluster generator</td>
694    </tr>
695    <tr>
696      <td>HiSeq 2000 A</td>
697      <td>Sequencer</td>
698    </tr>
699    <tr>
700      <td>Scanner A</td>
701      <td>Scanner</td>
702    </tr>
703    <tr>
704      <td>Print robot A</td>
705      <td>Print robot</td>
706    </tr>
707    </table>
708    <p>
709  </li>
710 
711  <li>
712    Create software (keep the 'Add as project default' option checked and the 'Replace existing default' unchecked):
713    <table class="listing" cellspacing="0" cellpadding="2" border="0">
714    <tr>
715      <th>Name</th>
716      <th>Type</th>
717    </tr>
718    <tr>
719      <td>Software A</td>
720      <td>Feature extraction</td>
721    </tr>
722    </table>
723    <p>
724  </li>
725
726  <li>
727    Create a reporter clone template:
728    <table class="listing" cellspacing="0" cellpadding="2" border="0">
729    <tr>
730      <th>Name</th>
731      <th>Properties</th>
732    </tr>
733    <tr>
734      <td>Template A</td>
735      <td>External ID, ID, Version, Sequence, Gene symbol</td>
736    </tr>
737    </table>
738    <p>
739  </li>
740 
741  <li>
742    Create bioplate type:
743    <table class="listing" cellspacing="0" cellpadding="2" border="0">
744    <tr>
745      <th>Name</th>
746      <th>Biomaterial type</th>
747      <th>Well lock mode</th>
748    </tr>
749    <tr>
750      <td>Bioplate type A</td>
751      <td>Any</td>
752      <td>Unlocked</td>
753    </tr>
754    </table>
755    <p>
756  </li>
757 
758  <li>
759    Create file formats (<i>i.e.</i>, plug-in configurations). The formats marked as
760    optional are not used in the test procedure, but may be useful to weed
761    out import problems, since they allow importing all info from the raw
762    data files. You may either enter the regular expressions as specified or
763    use the "Test with file" feature.
764   
765    <table class="listing" cellspacing="0" cellpadding="2" border="0">
766    <tr>
767      <th>Name</th>
768      <th>Plugin</th>
769      <th>Configuration values</th>
770    </tr>
771   
772    <tr class="oddrow">
773      <td>Plates for project A</td>
774      <td>Plate importer</td>
775      <td>
776     
777      <table border="0" cellspacing="0" cellpadding="2">
778      <tr>
779        <td><b>File</b></td>
780        <td><code>mouse/<br>plates_and_reporters.mouse.v4.37k.txt</code></td>
781      </tr>
782      <tr>
783        <td><i>Data header</i></td>
784        <td>384_number\t384_column\t384_row\t384_position\toligo_id.*</td>
785      </tr>
786      <tr>
787        <td><i>Data splitter</i></td>
788        <td>\t</td>
789      </tr>
790      <tr>
791        <td><i>Min data columns</i></td>
792        <td>5</td>
793      </tr>
794      <tr>
795        <td><i>Plate number/name</i></td>
796        <td>\384_number\</td>
797      </tr>
798      <tr>
799        <td><i>Row</i></td>
800        <td>\384_row\</td>
801      </tr>
802      <tr>
803        <td><i>Column</i></td>
804        <td>\384_column\</td>
805      </tr>
806      <tr>
807        <td><i>Reporter ID</i></td>
808        <td>\oligo_id\</td>
809      </tr>
810      </table>
811
812      </td>
813    </tr>
814   
815    <tr class="evenrow">
816      <td>GenePix feature importer<br>(optional)</td>
817      <td>Reporter map importer</td>
818      <td>
819     
820      <table border="0" cellspacing="0" cellpadding="2">
821      <tr>
822        <td><b>File</b></td>
823        <td><code>mouse/<br>genepix.mouse.v4.37k.00h.gpr</code></td>
824      </tr>
825      <tr>
826        <td><i>Data header</i></td>
827        <td>"Block"\t"Column"\t"Row"\t"Name"\t"ID"\t.*</td>
828      </tr>
829      <tr>
830        <td><i>Data splitter</i></td>
831        <td>\t</td>
832      </tr>
833      <tr>
834        <td><i>Min data columns</i></td>
835        <td>48</td>
836      </tr>
837      <tr>
838        <td><i>Max data columns</i></td>
839        <td>48</td>
840      </tr>
841      <tr>
842        <td><i>Reporter ID</i></td>
843        <td>\ID\</td>
844      </tr>
845      <tr>
846        <td><i>Block</i></td>
847        <td>\Block\</td>
848      </tr>
849      <tr>
850        <td><i>Column</i></td>
851        <td>\Column\</td>
852      </tr>
853      <tr>
854        <td><i>Row</i></td>
855        <td>\Row\</td>
856      </tr>
857      </table>
858
859      </td>
860    </tr>
861   
862    <tr class="oddrow">
863      <td>GTF features for project A</td>
864      <td>GTF reporter map importer</td>
865      <td>
866     
867      <table border="0" cellspacing="0" cellpadding="2">
868      <tr>
869        <td><b>File</b></td>
870        <td><code>sequencing/<br>UCSC_Human_hg19_RefSeqGenes.gtf</code></td>
871      </tr>
872      <tr>
873        <td><i>Data header</i></td>
874        <td>&lt;seqname&gt;\t.*&lt;transcript_id&gt;.*</td>
875      </tr>
876      <tr>
877        <td><i>Data splitter</i></td>
878        <td>\t</td>
879      </tr>
880      <tr>
881        <td><i>Min data columns</i></td>
882        <td>4</td>
883      </tr>
884      <tr>
885        <td><i>Remove quotes</i></td>
886        <td>yes</td>
887      </tr>
888      <tr>
889        <td><i>Complex mappings</i></td>
890        <td>allow</td>
891      </tr>
892      <tr>
893        <td><i>Reporter ID</i></td>
894        <td>\&lt;transcript_id&gt;\@\&lt;seqname&gt;\</td>
895      </tr>
896      <tr>
897        <td><i>Feature ID</i></td>
898        <td>\&lt;transcript_id&gt;\@\&lt;seqname&gt;\</td>
899      </tr>
900      </table>
901
902      </td>
903    </tr>
904   
905    <tr class="evenrow">
906      <td>Raw data for project A</td>
907      <td>Raw data importer</td>
908      <td>
909     
910      <table border="0" cellspacing="0" cellpadding="2">
911      <tr>
912        <td><b>File</b></td>
913        <td><code>mouse/<br>genepix.mouse.v4.37k.00h.gpr</code></td>
914      </tr>
915      <tr>
916        <td><i>Raw data type</i></td>
917        <td>Genepix</td>
918      </tr>
919      <tr>
920        <td><i>Header</i></td>
921        <td>"(.+)=(.*)"</td>
922      </tr>
923      <tr>
924        <td><i>Data header</i></td>
925        <td>"Block"\t"Column"\t"Row"\t"Name"\t"ID"\t.*"Ratio of Medians \(532\/635\)".*</td>
926      </tr>
927      <tr>
928        <td><i>Data splitter</i></td>
929        <td>\t</td>
930      </tr>
931      <tr>
932        <td><i>Min data columns</i></td>
933        <td>48</td>
934      </tr>
935      <tr>
936        <td><i>Max data columns</i></td>
937        <td>48</td>
938      </tr>
939
940      <tr>
941        <td><i>Block</i></td>
942        <td>\Block\</td>
943      </tr>
944      <tr>
945        <td><i>Column</i></td>
946        <td>\Column\</td>
947      </tr>
948      <tr>
949        <td><i>Row</i></td>
950        <td>\Row\</td>
951      </tr>
952      <tr>
953        <td><i>X</i></td>
954        <td>\X\</td>
955      </tr>
956      <tr>
957        <td><i>Y</i></td>
958        <td>\Y\</td>
959      </tr>
960      <tr>
961        <td><i>Reporter ID</i></td>
962        <td>\ID\</td>
963      </tr>
964      <tr>
965        <td><i>Spot diameter</i></td>
966        <td>\Dia.\</td>
967      </tr>
968      <tr>
969        <td><i>Channel 1 foreground median</i></td>
970        <td>\F635 Median\</td>
971      </tr>
972      <tr>
973        <td><i>Channel 1 foreground mean</i></td>
974        <td>\F635 Mean\</td>
975      </tr>
976      <tr>
977        <td><i>Channel 1 foreground standard deviation</i></td>
978        <td>\F635 SD\</td>
979      </tr>
980      <tr>
981        <td><i>Channel 1 background median</i></td>
982        <td>\B635 Median\</td>
983      </tr>
984      <tr>
985        <td><i>Channel 1 background mean</i></td>
986        <td>\B635 Mean\</td>
987      </tr>
988      <tr>
989        <td><i>Channel 1 background standard deviation</i></td>
990        <td>\B635 SD\</td>
991      </tr>
992      <tr>
993        <td><i>Percent pixels within 1 standard deviation</i></td>
994        <td>\% > B635+1SD\</td>
995      </tr>
996      <tr>
997        <td><i>Percent pixels within 2 standard deviations</i></td>
998        <td>\% > B635+2SD\</td>
999      </tr>
1000      <tr>
1001        <td><i>Percent saturated pixels</i></td>
1002        <td>\F635 % Sat.\</td>
1003      </tr>
1004      <tr>
1005        <td><i>Channel 2 foreground median</i></td>
1006        <td>\F532 Median\</td>
1007      </tr>
1008      <tr>
1009        <td><i>Channel 2 foreground mean</i></td>
1010        <td>\F532 Mean\</td>
1011      </tr>
1012      <tr>
1013        <td><i>Channel 2 foreground standard deviation</i></td>
1014        <td>\F532 SD\</td>
1015      </tr>
1016      <tr>
1017        <td><i>Channel 2 background median</i></td>
1018        <td>\B532 Median\</td>
1019      </tr>
1020      <tr>
1021        <td><i>Channel 2 background mean</i></td>
1022        <td>\B532 Mean\</td>
1023      </tr>
1024      <tr>
1025        <td><i>Channel 2 background standard deviation</i></td>
1026        <td>\B532 SD\</td>
1027      </tr>
1028      <tr>
1029        <td><i>Percent pixels within 1 standard deviation</i></td>
1030        <td>\% > B532+1SD\</td>
1031      </tr>
1032      <tr>
1033        <td><i>Percent pixels within 2 standard deviations</i></td>
1034        <td>\% > B532+2SD\</td>
1035      </tr>
1036      <tr>
1037        <td><i>Percent saturated pixels</i></td>
1038        <td>\F532 % Sat.\</td>
1039      </tr>
1040      <tr>
1041        <td><i>Foreground pixels</i></td>
1042        <td>\F Pixels\</td>
1043      </tr>
1044      <tr>
1045        <td><i>Background pixels</i></td>
1046        <td>\B Pixels\</td>
1047      </tr>
1048      <tr>
1049        <td><i>Flags</i></td>
1050        <td>\Flags\</td>
1051      </tr>
1052      </table>
1053
1054      </td>
1055    </tr>
1056   
1057    <tr class="oddrow">
1058      <td>Raw data for project A (dye-swap)</td>
1059      <td>Raw data importer</td>
1060      <td>
1061
1062      <table border="0" cellspacing="0" cellpadding="2">
1063      <tr>
1064        <td><b>File</b></td>
1065        <td><code>mouse/<br>genepix.mouse.v4.37k.00h.dyeswap.gpr</code></td>
1066      </tr>
1067      <tr>
1068        <td><i>Raw data type</i></td>
1069        <td>Genepix</td>
1070      </tr>
1071      <tr>
1072        <td><i>Header</i></td>
1073        <td>"(.+)=(.*)"</td>
1074      </tr>
1075      <tr>
1076        <td><i>Data header</i></td>
1077        <td>"Block"\t"Column"\t"Row"\t"Name"\t"ID"\t.*"Ratio of Medians \(635\/532\)".*</td>
1078      </tr>
1079      <tr>
1080        <td><i>Data splitter</i></td>
1081        <td>\t</td>
1082      </tr>
1083      <tr>
1084        <td><i>Min data columns</i></td>
1085        <td>48</td>
1086      </tr>
1087      <tr>
1088        <td><i>Max data columns</i></td>
1089        <td>48</td>
1090      </tr>
1091
1092      <tr>
1093        <td><i>Block</i></td>
1094        <td>\Block\</td>
1095      </tr>
1096      <tr>
1097        <td><i>Column</i></td>
1098        <td>\Column\</td>
1099      </tr>
1100      <tr>
1101        <td><i>Row</i></td>
1102        <td>\Row\</td>
1103      </tr>
1104      <tr>
1105        <td><i>X</i></td>
1106        <td>\X\</td>
1107      </tr>
1108      <tr>
1109        <td><i>Y</i></td>
1110        <td>\Y\</td>
1111      </tr>
1112      <tr>
1113        <td><i>Reporter ID</i></td>
1114        <td>\ID\</td>
1115      </tr>
1116      <tr>
1117        <td><i>Spot diameter</i></td>
1118        <td>\Dia.\</td>
1119      </tr>
1120      <tr>
1121        <td><i>Channel 1 foreground median</i></td>
1122        <td>\F532 Median\</td>
1123      </tr>
1124      <tr>
1125        <td><i>Channel 1 foreground mean</i></td>
1126        <td>\F532 Mean\</td>
1127      </tr>
1128      <tr>
1129        <td><i>Channel 1 foreground standard deviation</i></td>
1130        <td>\F532 SD\</td>
1131      </tr>
1132      <tr>
1133        <td><i>Channel 1 background median</i></td>
1134        <td>\B532 Median\</td>
1135      </tr>
1136      <tr>
1137        <td><i>Channel 1 background mean</i></td>
1138        <td>\B532 Mean\</td>
1139      </tr>
1140      <tr>
1141        <td><i>Channel 1 background standard deviation</i></td>
1142        <td>\B532 SD\</td>
1143      </tr>
1144      <tr>
1145        <td><i>Percent pixels within 1 standard deviation</i></td>
1146        <td>\% > B532+1SD\</td>
1147      </tr>
1148      <tr>
1149        <td><i>Percent pixels within 2 standard deviations</i></td>
1150        <td>\% > B532+2SD\</td>
1151      </tr>
1152      <tr>
1153        <td><i>Percent saturated pixels</i></td>
1154        <td>\F532 % Sat.\</td>
1155      </tr>
1156      <tr>
1157        <td><i>Channel 2 foreground median</i></td>
1158        <td>\F635 Median\</td>
1159      </tr>
1160      <tr>
1161        <td><i>Channel 2 foreground mean</i></td>
1162        <td>\F635 Mean\</td>
1163      </tr>
1164      <tr>
1165        <td><i>Channel 2 foreground standard deviation</i></td>
1166        <td>\F635 SD\</td>
1167      </tr>
1168      <tr>
1169        <td><i>Channel 2 background median</i></td>
1170        <td>\B635 Median\</td>
1171      </tr>
1172      <tr>
1173        <td><i>Channel 2 background mean</i></td>
1174        <td>\B635 Mean\</td>
1175      </tr>
1176      <tr>
1177        <td><i>Channel 2 background standard deviation</i></td>
1178        <td>\B635 SD\</td>
1179      </tr>
1180      <tr>
1181        <td><i>Percent pixels within 1 standard deviation</i></td>
1182        <td>\% > B635+1SD\</td>
1183      </tr>
1184      <tr>
1185        <td><i>Percent pixels within 2 standard deviations</i></td>
1186        <td>\% > B635+2SD\</td>
1187      </tr>
1188      <tr>
1189        <td><i>Percent saturated pixels</i></td>
1190        <td>\F635 % Sat.\</td>
1191      </tr>
1192      <tr>
1193        <td><i>Foreground pixels</i></td>
1194        <td>\F Pixels\</td>
1195      </tr>
1196      <tr>
1197        <td><i>Background pixels</i></td>
1198        <td>\B Pixels\</td>
1199      </tr>
1200      <tr>
1201        <td><i>Flags</i></td>
1202        <td>\Flags\</td>
1203      </tr>
1204      </table>
1205
1206      </td>
1207    </tr>
1208    </table>
1209    <p>
1210  </li>
1211 
1212  <li>
1213    Annotate the file formats:
1214    <table class="listing" cellspacing="0" cellpadding="2" border="0">
1215    <tr>
1216      <th>File format</th>
1217      <th>Annotation</th>
1218      <th>Value</th>
1219    </tr>
1220    <tr>
1221      <td>Raw data for project A</td>
1222      <td>Dye swap</td>
1223      <td>false</td>
1224    </tr>
1225    <tr>
1226      <td>Raw data for project A (dye swap)</td>
1227      <td>Dye swap</td>
1228      <td>true</td>
1229    </tr>
1230    </table>
1231    This will make the raw data importer automatically annotate the
1232    raw bioassays with the specified annotations.
1233    <p>
1234  </li>
1235 
1236  <li>
1237    Create plate type:
1238    <table class="listing" cellspacing="0" cellpadding="2" border="0">
1239    <tr>
1240      <th>Name</th>
1241      <th>Geometry</th>
1242    </tr>
1243    <tr>
1244      <td>Plate type A</td>
1245      <td>384-well (16 x 24)</td>
1246    </tr>
1247    </table>
1248    <p>
1249  </li>
1250 
1251  <li>
1252    Import plates:
1253    <ol>
1254    <li>Go to the <code>Array LIMS -> Plates</code> page.</li>
1255    <li>Click on the <code>Import</code> button.</li>
1256    <li>Choose <code>auto-detect</code> and select
1257      the file <code>plates_and_reporters.mouse.v4.37k.txt</code>.</li>
1258    <li>The <code>Plates for project A</code> format should be
1259      found.</li>
1260    <li>Specify the following parameters:
1261   
1262      <table border="0" cellspacing="0" cellpadding="2">
1263      <tr>
1264        <td><i>Plate type</i></td>
1265        <td>Plate type A</td>
1266      </tr>
1267      <tr>
1268        <td><i>Plate name prefix</i></td>
1269        <td>Plate A</td>
1270      </tr>
1271      <tr>
1272        <td><i>Plate name padding</i></td>
1273        <td>4</td>
1274      </tr>
1275      </table>
1276    </li>
1277    <li>Continue and wait for the import to finish. It should create 96 plates.</li>
1278    </ol>
1279    <p>
1280  </li>
1281
1282  <li>
1283    Create array designs and upload data files to them.  Keep the 'Set as project default' option checked
1284    if doing this manually.
1285    <table class="listing" cellspacing="0" cellpadding="2" border="0">
1286    <tr>
1287      <th>Name</th>
1288      <th>Platform/Variant</th>
1289      <th>File(s)</th>
1290    </tr>
1291    <tr>
1292      <td>Array design A</td>
1293      <td>Generic</td>
1294      <td><i>Print map</i>: <code>mouse/printmap.mouse.v4.37k.tam</code></td>
1295    </tr>
1296    <tr>
1297      <td>Affymetrix A</td>
1298      <td>Affymetrix</td>
1299      <td><i>CDF file</i>: <code>affymtrix/cdf/MG_U74Av2.cdf</code></td>
1300    </tr>
1301    <tr>
1302      <td>RefSeqDesign A</td>
1303      <td>Sequencing/Expression-like</td>
1304      <td><i>GTF ref-seq file</i>: <code>sequencing/UCSC_Human_hg19_RefSeqGenes.gtf</code></td>
1305    </tr>
1306    </table>
1307    <p>
1308    Or
1309    <p>
1310    Import array designs with the ArrayDesignImporter plug-in.
1311    <ol>
1312      <li>Make sure the data-files, mentioned in table above, are located in <code>/home/power/</code>, upload them if not</li>
1313      <li>Click on the <code>Import</code> button on the array design list page.</li>
1314      <li>Choose ArrayDesignImporter in the plug-in drop-down list.</li>
1315      <li><b>Test with file:</b> <code>arraydesign_out.txt</code> and set
1316        the parsing parameters with help of the <code>Auto generate</code> button on the <code>Column mapping</code>
1317        tab.</li>
1318      <li>Start the import-job by clicking on the <code>Finish</code> button on the third wizard-page.</li>     
1319    </ol>
1320    <p>
1321  </li>
1322 
1323  <li>
1324    Connect <code>Array design A</code> with plates. Select the imported plates (plate names starting
1325    with <code>Plate A</code>) and sort them in the correct order (as indicated by their names).
1326    <p>
1327  </li>
1328 
1329  <li>
1330    Import features to Array design A:
1331    <ol>
1332    <li>Click on the <code>Import</code> button when viewing properties for the array design.</li>
1333    <li>Choose <code>auto-detect</code> and use the file
1334      <code>printmap.mouse.v4.37k.tam</code>.</li>
1335    <li>The <code>Print map importer</code> plug-in should be
1336      found.</li>
1337    <li>Continue and wait for the import to finish. It should create 36,864 features and 48 blocks.</li>
1338    </ol>
1339    <p>
1340    Import features to RefSeqDesign A:
1341    <ol>
1342    <li>Click on the <code>Import</code> button when viewing properties for the array design.</li>
1343    <li>Choose <code>auto-detect</code> and use the file
1344      <code>UCSC_Human_hg19_RefSeqGenes.gtf</code>.</li>
1345    <li>The <code>GTF reporter map importer</code> plug-in should be
1346      found. Select the <code>GTF features for project A</code> format.</li>
1347    <li>Continue and wait for the import to finish. It should create 38,977 features and 1 block.</li>
1348    </ol>
1349    <p>
1350  </li>
1351
1352  <li>
1353    Set project defaults. Go to the projects page and edit the
1354    <code>Project A</code> project. On the <code>Defaults</code>
1355    tab, set the following defaults. NOTE! Most of the items in this
1356    list should already be registered as default items if the
1357    'Add as project default' option was used when creating the new items.
1358   
1359    <table class="listing" cellspacing="0" cellpadding="2" border="0">
1360    <tr>
1361      <th>Setting</th>
1362      <th>Value(s)</th>
1363    </tr>
1364    <tr>
1365      <td>Raw data type</td>
1366      <td>Genepix</td>
1367    </tr>
1368    <tr>
1369      <td>Platforms</td>
1370      <td>
1371        Generic<br>
1372        Affymetrix
1373      </td>
1374    </tr>
1375    <tr>
1376      <td>Platforms variants</td>
1377      <td>
1378        Sequencing / Expression-like
1379      </td>
1380    </tr>
1381    <tr>
1382      <td>Array designs</td>
1383      <td>
1384        Array design A<br>
1385        Affymetrix A<br>
1386        RefSeqDesign A
1387      </td>
1388    </tr>
1389    <tr>
1390      <td>Protocols</td>
1391      <td>
1392        Sampling A<br>
1393        Extraction A<br>
1394        Labeling A<br>
1395        Library preparation A<br>
1396        Hybridization A<br>
1397        cBot Settings A<br>
1398        Scanning A<br>
1399        HiSeq Settings A<br>
1400        TopHat Settings A<br>
1401        Feature extraction A<br>
1402        Cufflinks Settings A<br>
1403        Printing A
1404      </td>
1405    </tr>
1406    <tr>
1407      <td>Hardware</td>
1408      <td>
1409        Hybridization station A<br>
1410        cBot A<br>
1411        HiSeq 2000 A<br>
1412        Scanner A<br>
1413        Print robot A
1414      </td>
1415    </tr>
1416    <tr>
1417      <td>Software</td>
1418      <td>
1419        Software A<br>
1420        TopHat<br>
1421        Cufflinks
1422      </td>
1423    </tr>
1424    </table>
1425   
1426    <p>
1427  </li>
1428
1429  <li>
1430    Create array batches:
1431    <table class="listing" cellspacing="0" cellpadding="2" border="0">
1432    <tr>
1433      <th>Name</th>
1434      <th>Array design</th>
1435      <th>Print robot</th>
1436      <th>Protocol</th>
1437    </tr>
1438    <tr>
1439      <td>Array batch A</td>
1440      <td>Array design A</td>
1441      <td>Print robot A</td>
1442      <td>Printing A</td>
1443    </tr>
1444    <tr>
1445      <td>Affymetrix batch A</td>
1446      <td>Affymetrix A</td>
1447      <td></td>
1448      <td></td>
1449    </tr>
1450    </table>
1451    <p>
1452    Or
1453    <p>
1454    Import array batches with the ArrayBatchImporter plug-in.
1455    <ol>
1456      <li>Click on the <code>Import</code> button on the array batch list page.</li>
1457      <li>Select ArrayBatchImporter in the plug-in drop-down list and click <code>Next</code></li>
1458      <li><b>Test with file:</b> <code>arraybatch_out.txt</code> and set  the parsing parameters
1459        with help of the <code>Auto generate</code> button on the <code>Column mapping</code>
1460        tab.</li>
1461      <li>Start the import-job by clicking on the <code>Finish</code> button on the third wizzard-page.</li>     
1462    </ol>
1463    <p>   
1464  </li>
1465
1466  <li>
1467    Create array slides with the <code>Create slides</code>
1468    wizard.
1469   
1470    <table class="listing" cellspacing="0" cellpadding="2" border="0">
1471    <tr>
1472      <th>Name</th>
1473      <th>Array batch</th>
1474      <th>Quantity</th>
1475    </tr>
1476    <tr>
1477      <td>Array slide A.</td>
1478      <td>Array batch A</td>
1479      <td>4</td>
1480    </tr>
1481    <tr>
1482      <td>Affymetrix slide A.</td>
1483      <td>Affymetrix batch A</td>
1484      <td>3</td>
1485    </tr>
1486    </table>
1487    <p>
1488    Or
1489    <p>
1490    Import array slides with the ArraySlideImporter plug-in.
1491    <ol>
1492      <li>Click on the <code>Import</code> button on the array slide list page.</li>
1493      <li>Select ArraySlideImporter in the plug-in drop-down list and click <code>Next</code></li>
1494      <li><b>Test with file:</b> <code>arrayslide_out.txt</code> and set  the parsing parameters
1495        with help of the <code>Auto generate</code> button on the <code>Column mapping</code>
1496        tab.</li>
1497      <li>Start the import-job by clicking on the <code>Finish</code> button on the third wizzard-page.</li>     
1498    </ol>
1499    <p>
1500  </li>
1501  </ol>
1502
1503  <a name="user"></a>
1504  <h2>5. User tests</h2>
1505  <p>
1506    The user is a typical worker in the project. The user does the actual experimentation in the
1507    lab, which includes collecting samples, doing extraction, labeling and hybridizations.
1508    The user also scans and analyses the raw data resulting from the images. Inserting items can be
1509    done in two different ways, .
1510  </p>
1511  <h3>First step</h3>
1512 
1513  <ol>
1514  <li>Activate the <code>Project A</code> project.
1515    <p>
1516   
1517  <li>
1518    Create a bioplate:
1519    <table class="listing" cellspacing="0" cellpadding="2" border="0">
1520    <tr>
1521      <th>Name</th>
1522      <th>Plate geometry</th>
1523      <th>Bioplate type</th>
1524    </tr>
1525    <tr>
1526      <td>Bioplate A</td>
1527      <td>96-well (8 x 12)</td>
1528      <td>BioPlate type A</td>
1529    </tr>
1530    </table>
1531    <p>
1532    <li>Continue with the second step, which can be done with batch importers or
1533      manually.
1534   
1535  </ol>
1536 
1537 
1538  <h3>Second step (using batch importers)</h3>
1539
1540  <ol>
1541    <li>Click on the <code>Import</code> button on the list page.</li>
1542    <li>Select &lt;itemtype&gt;Importer in the plug-in drop-down list and click <code>Next</code></li>
1543    <li><b>Test with file:</b> using the right file(listed below) and set the parsing parameters
1544      by using the <code>Auto generate</code> button on the <code>Column mapping</code> tab.
1545      <table class="listing" cellspacing="0" cellpadding="2" border="0">
1546      <tr>
1547        <th>Itemtype</th>
1548        <th>File</th>
1549      </tr>
1550      <tr>
1551        <td>Biosource</td>
1552        <td>biosource_out.txt</td>       
1553      </tr>
1554      <tr>
1555        <td>Samples</td>
1556        <td>sample_out.txt</td>
1557      </tr>
1558      <tr>
1559        <td>Extracts (including labeled extracts and libraries)</td>
1560        <td>extract_out.txt</td>
1561      </tr>
1562      <tr>
1563        <td>Physical bioassays (hybridizations, flow cells)</td>
1564        <td>physicalbioassay_out.txt</td>
1565      </tr>
1566      <tr>
1567        <td>Derived bioassays (scans, assemblys)</td>
1568        <td>derivedbioassay_out.txt</td>
1569      </tr>
1570      <tr>
1571        <td>Raw bioassays</td>
1572        <td>rawbioassay_out.txt</td>
1573      </tr>
1574      </table>
1575      The files listed for biosource, samples, extracts, and derived bioassays also contain annotations
1576      for the items and these files should also be used with the annotation importer.
1577      The procedure is the same as for batch importers except that only <code>\Name\</code>
1578      is needed in the column mapping. The annotation column should be selected by default in
1579      the second wizard-step.
1580    </li>
1581    <li>Start the import-job by clicking on the <code>Finish</code> button on the third wizard-page.</li>
1582    <li>Continue with <a href="#step3">the third step</a>.</li>     
1583  </ol>
1584 
1585  <h3>Second step (create items manually)</h3>
1586  <ol>
1587  <li>
1588    Create a biosource:
1589    <table class="listing" cellspacing="0" cellpadding="2" border="0">
1590    <tr>
1591      <th>Name</th>
1592      <th>Annotations</th>
1593    </tr>
1594    <tr>
1595      <td>Biosource A</td>
1596      <td>
1597        <table border="0" cellspacing="0" cellpadding="2">
1598        <tr>
1599          <td><i>Drug resistance:</i></td>
1600          <td>medium</td>
1601        </tr>
1602        </table>
1603      </td>
1604    </tr>
1605    </table>
1606    <p>
1607  </li>
1608 
1609  <li>
1610    Create samples:
1611    <table class="listing" cellspacing="0" cellpadding="2" border="0">
1612    <tr>
1613      <th>Name</th>
1614      <th>Protocol</th>
1615      <th>Biosource</th>
1616      <th>Bioplate [well]</th>
1617      <th>Annotations</th>
1618    </tr>
1619    <tr>
1620      <td>Sample A.00h</td>
1621      <td>Sampling A</td>
1622      <td>Biosource A</td>
1623      <td>Bioplate A [A1]</td>
1624      <td>
1625        <table border="0" cellspacing="0" cellpadding="2">
1626        <tr>
1627          <td><i>Time:</i></td>
1628          <td>0h</td>
1629        </tr>
1630        </table>
1631      </td>
1632    </tr>
1633    <tr>
1634      <td>Sample A.24h</td>
1635      <td>Sampling A</td>
1636      <td>Biosource A</td>
1637      <td>Bioplate A [A2]</td>
1638      <td>
1639        <table border="0" cellspacing="0" cellpadding="2">
1640        <tr>
1641          <td><i>Time:</i></td>
1642          <td>24h</td>
1643        </tr>
1644        </table>
1645      </td>
1646    </tr>
1647    <tr>
1648      <td>Sample A.ref</td>
1649      <td>Sampling A</td>
1650      <td>-</td>
1651      <td>Bioplate A [A3]</td>
1652      <td>-</td>
1653    </tr>
1654    </table>
1655    <p>
1656  </li>
1657
1658  <li>
1659    Create extracts:
1660    <table class="listing" cellspacing="0" cellpadding="2" border="0">
1661    <tr>
1662      <th>Name</th>
1663      <th>Type</th>
1664      <th>Protocol</th>
1665      <th>Parent</th>
1666      <th>Bioplate [well]</th>
1667      <th>Annotations</th>
1668    </tr>
1669    <tr>
1670      <td>Extract A.00h</td>
1671      <td>-</td>
1672      <td>Extraction A</td>
1673      <td>Sample A.00h</td>
1674      <td>Bioplate A [B1]</td>
1675      <td>-</td>
1676    </tr>
1677    <tr>
1678      <td>Extract A.24h</td>
1679      <td>-</td>
1680      <td>Extraction A</td>
1681      <td>Sample A.24h</td>
1682      <td>Bioplate A [B2]</td>
1683      <td>-</td>
1684    </tr>
1685    <tr>
1686      <td>Extract A.ref</td>
1687      <td>-</td>
1688      <td>Extraction A</td>
1689      <td>Sample A.ref</td>
1690      <td>Bioplate A [B3]</td>
1691      <td>-</td>
1692    </tr>
1693    <tr>
1694      <td>Extract A.00h.qc</td>
1695      <td>Quality control</td>
1696      <td>-</td>
1697      <td>Extract A.00h</td>
1698      <td>-</td>
1699      <td>
1700        <table border="0" cellspacing="0" cellpadding="2">
1701        <tr>
1702          <td><i>RIN:</i></td>
1703          <td>8.1</td>
1704        </tr>
1705        </table>
1706      </td>
1707    </tr>
1708    <tr>
1709      <td>Extract A.24h.qc</td>
1710      <td>Quality control</td>
1711      <td>-</td>
1712      <td>Extract A.24h</td>
1713      <td>-</td>
1714      <td>
1715        <table border="0" cellspacing="0" cellpadding="2">
1716        <tr>
1717          <td><i>RIN:</i></td>
1718          <td>8.5</td>
1719        </tr>
1720        </table>
1721      </td>
1722    </tr>
1723    <tr>
1724      <td>Extract A.ref.qc</td>
1725      <td>Quality control</td>
1726      <td>-</td>
1727      <td>Extract A.ref</td>
1728      <td>-</td>
1729      <td>
1730        <table border="0" cellspacing="0" cellpadding="2">
1731        <tr>
1732          <td><i>RIN:</i></td>
1733          <td>9.2</td>
1734        </tr>
1735        </table>
1736      </td>
1737    </tr>
1738    </table>
1739    <p>
1740  </li>
1741
1742  <li>
1743    Create labeled extracts and libraries:
1744    <table class="listing" cellspacing="0" cellpadding="2" border="0">
1745    <tr>
1746      <th>Name</th>
1747      <th>Type</th>
1748      <th>Label</th>
1749      <th>Protocol</th>
1750      <th>Extract</th>
1751      <th>Bioplate [well]</th>
1752    </tr>
1753    <tr>
1754      <td>Labeled extract A.00h</td>
1755      <td>Labeled extract</td>
1756      <td>cy3</td>
1757      <td>Labeling A</td>
1758      <td>Extract A.00h</td>
1759      <td>Bioplate A [C1]</td>
1760    </tr>
1761    <tr>
1762      <td>Labeled extract A.24h</td>
1763      <td>Labeled extract</td>
1764      <td>cy3</td>
1765      <td>Labeling A</td>
1766      <td>Extract A.24h</td>
1767      <td>Bioplate A [C2]</td>
1768    </tr>
1769    <tr>
1770      <td>Labeled extract A.ref</td>
1771      <td>Labeled extract</td>
1772      <td>cy5</td>
1773      <td>Labeling A</td>
1774      <td>Extract A.ref</td>
1775      <td>Bioplate A [C3]</td>
1776    </tr>
1777    <tr class="shaded">
1778      <td>Labeled extract A.00h (dye-swap)</td>
1779      <td>Labeled extract</td>
1780      <td>cy5</td>
1781      <td>Labeling A</td>
1782      <td>Extract A.00h</td>
1783      <td>Bioplate A [D1]</td>
1784    </tr>
1785    <tr class="shaded">
1786      <td>Labeled extract A.24h (dye-swap)</td>
1787      <td>Labeled extract</td>
1788      <td>cy5</td>
1789      <td>Labeling A</td>
1790      <td>Extract A.24h</td>
1791      <td>Bioplate A [D2]</td>
1792    </tr>
1793    <tr class="shaded">
1794      <td>Labeled extract A.ref (dye-swap)</td>
1795      <td>Labeled extract</td>
1796      <td>cy3</td>
1797      <td>Labeling A</td>
1798      <td>Extract A.ref</td>
1799      <td>Bioplate A [D3]</td>
1800    </tr>
1801    <tr>
1802      <td>Library A.00h</td>
1803      <td>Library</td>
1804      <td>-</td>
1805      <td>Library preparation A</td>
1806      <td>Extract A.00h</td>
1807      <td>Bioplate A [E1]</td>
1808    </tr>
1809    <tr>
1810      <td>Library A.24h</td>
1811      <td>Library</td>
1812      <td>-</td>
1813      <td>Library preparation A</td>
1814      <td>Extract A.24h</td>
1815      <td>Bioplate A [E2]</td>
1816    </tr>
1817    </table>
1818    <p>
1819  </li>
1820
1821  <li>
1822    Create physical bioassays (hybridizations and flow cells):
1823    <table class="listing" cellspacing="0" cellpadding="2" border="0">
1824    <tr>
1825      <th>Name</th>
1826      <th>Protocol</th>
1827      <th>Hardware</th>
1828      <th>Array slide</th>
1829      <th>Extracts (position)</th>
1830    </tr>
1831    <tr>
1832      <td>Hybridization A.00h</td>
1833      <td>Hybridization A</td>
1834      <td>Hybridization station A</td>
1835      <td>Array slide A.1</td>
1836      <td>Labeled extract A.00h,<br>Labeled extract A.ref</td>
1837    </tr>
1838    <tr>
1839      <td>Hybridization A.24h</td>
1840      <td>Hybridization A</td>
1841      <td>Hybridization station A</td>
1842      <td>Array slide A.2</td>
1843      <td>Labeled extract A.24h,<br>Labeled extract A.ref</td>
1844    </tr>
1845    <tr class="shaded">
1846      <td>Hybridization A.00h (dye-swap)</td>
1847      <td>Hybridization A</td>
1848      <td>Hybridization station A</td>
1849      <td>Array slide A.3</td>
1850      <td>Labeled extract A.00h (dye-swap),<br>Labeled extract A.ref (dye-swap)</td>
1851    </tr>
1852    <tr class="shaded">
1853      <td>Hybridization A.24h (dye-swap)</td>
1854      <td>Hybridization A</td>
1855      <td>Hybridization station A</td>
1856      <td>Array slide A.4</td>
1857      <td>Labeled extract A.24h (dye-swap),<br>Labeled extract A.ref (dye-swap)</td>
1858    </tr>
1859    <tr>
1860      <td>Affymetrix hyb A.1</td>
1861      <td>Hybridization A</td>
1862      <td>Hybridization station A</td>
1863      <td>Affymetrix slide A.1</td>
1864      <td>Labeled extract A.00h</td>
1865    </tr>
1866    <tr>
1867      <td>Affymetrix hyb A.2</td>
1868      <td>Hybridization A</td>
1869      <td>Hybridization station A</td>
1870      <td>Affymetrix slide A.2</td>
1871      <td>Labeled extract A.24h</td>
1872    </tr>
1873    <tr>
1874      <td>Affymetrix hyb A.3</td>
1875      <td>Hybridization A</td>
1876      <td>Hybridization station A</td>
1877      <td>Affymetrix slide A.3</td>
1878      <td>Labeled extract A.ref</td>
1879    </tr>
1880    <tr class="shaded">
1881      <td>Flow cell A</td>
1882      <td>cBot Settings A</td>
1883      <td>cBot A</td>
1884      <td>-</td>
1885      <td>Library A.00h (1),<br>Library A.24h (2)</td>
1886    </tr>
1887    </table>
1888    <p>
1889  </li>
1890 
1891  <li>
1892    Create derived bioassays (scans, arrangements, etc.):
1893    <table class="listing" cellspacing="0" cellpadding="2" border="0">
1894    <tr>
1895      <th>Name</th>
1896      <th>Parent bioasasay</th>
1897      <th>Parent extract</th>
1898      <th>Hardware/Software</th>
1899      <th>Protocol</th>
1900      <th>PMT gain</th>
1901    </tr>
1902    <tr>
1903      <td>Scan A.00h</td>
1904      <td>Hybridization A.00h</td>
1905      <td>-</td>
1906      <td>HW: Scanner A</td>
1907      <td>Scanning A</td>
1908      <td>400 V</td>
1909    </tr>
1910    <tr>
1911      <td>Scan A.24h</td>
1912      <td>Hybridization A.24h</td>
1913      <td>-</td>
1914      <td>HW: Scanner A</td>
1915      <td>Scanning A</td>
1916      <td>500 V</td>
1917    </tr>
1918    <tr class="shaded">
1919      <td>Scan A.00h (dye-swap)</td>
1920      <td>Hybridization A.00h (dye-swap)</td>
1921      <td>-</td>
1922      <td>HW: Scanner A</td>
1923      <td>Scanning A</td>
1924      <td>600 V</td>
1925    </tr>
1926    <tr class="shaded">
1927      <td>Scan A.24h (dye-swap)</td>
1928      <td>Hybridization A.24h (dye-swap)</td>
1929      <td>-</td>
1930      <td>HW: Scanner A</td>
1931      <td>Scanning A</td>
1932      <td>700 V</td>
1933    </tr>
1934    <tr>
1935      <td>Affymetrix scan A.1</td>
1936      <td>Affymetrix hyb A.1</td>
1937      <td>-</td>
1938      <td>HW: Scanner A</td>
1939      <td>Scanning A</td>
1940      <td>800 V</td>
1941    </tr>
1942    <tr>
1943      <td>Affymetrix scan A.2</td>
1944      <td>Affymetrix hyb A.2</td>
1945      <td>-</td>
1946      <td>HW: Scanner A</td>
1947      <td>Scanning A</td>
1948      <td>900 V</td>
1949    </tr>
1950    <tr>
1951      <td>Affymetrix scan A.3</td>
1952      <td>Affymetrix hyb A.3</td>
1953      <td>-</td>
1954      <td>HW: Scanner A</td>
1955      <td>Scanning A</td>
1956      <td>1000 V</td>
1957    </tr>
1958    <tr class="shaded">
1959      <td>Sequenced A</td>
1960      <td>Flow cell A</td>
1961      <td>-</td>
1962      <td>HW: HiSeq 2000 A</td>
1963      <td>HiSeq Settings A</td>
1964      <td>-</td>
1965    </tr>
1966    <tr class="shaded">
1967      <td>Arrangement A.00h</td>
1968      <td>Sequenced A</td>
1969      <td>Library A.00h</td>
1970      <td>SW: TopHat</td>
1971      <td>TopHat Settings A</td>
1972      <td>-</td>
1973    </tr>
1974    <tr class="shaded">
1975      <td>Arrangement A.24h</td>
1976      <td>Sequenced A</td>
1977      <td>Library A.24h</td>
1978      <td>SW: TopHat</td>
1979      <td>TopHat Settings A</td>
1980      <td>-</td>
1981    </tr>
1982    </table>
1983    <p>
1984  </li>
1985 
1986  <li>
1987    Create raw bioassays:
1988    <table class="listing" cellspacing="0" cellpadding="2" border="0">
1989    <tr>
1990      <th>Name</th>
1991      <th>Platform/Raw data type</th>
1992      <th>Parent bioassay</th>
1993      <th>Parent extract</th>
1994      <th>Array design</th>
1995      <th>Protocol</th>
1996      <th>Software</th>
1997      <th>File(s)</th>
1998    </tr>
1999    <tr>
2000      <td>Raw bioassay A.00h</td>
2001      <td>Generic/GenePix</td>
2002      <td>Scan A.00h</td>
2003      <td>-</td>
2004      <td>Array design A</td>
2005      <td>Feature extraction A</td>
2006      <td>Software A</td>
2007      <td><i>Raw data</i>: <code>mouse/genepix.mouse.v4.37k.00h.gpr</code></td>
2008    </tr>
2009    <tr>
2010      <td>Raw bioassay A.24h</td>
2011      <td>Generic/GenePix</td>
2012      <td>Scan A.24h</td>
2013      <td>-</td>
2014      <td>Array design A</td>
2015      <td>Feature extraction A</td>
2016      <td>Software A</td>
2017      <td><i>Raw data</i>: <code>mouse/genepix.mouse.v4.37k.24h.gpr</code></td>
2018    </tr>   
2019    <tr class="shaded">
2020      <td>Raw bioassay A.00h (dye-swap)</td>
2021      <td>Generic/GenePix</td>
2022      <td>Scan A.00h (dye-swap)</td>
2023      <td>-</td>
2024      <td>Array design A</td>
2025      <td>Feature extraction A</td>
2026      <td>Software A</td>
2027      <td><i>Raw data</i>: <code>mouse/genepix.mouse.v4.37k.00h.dyeswap.gpr</code></td>
2028    </tr> 
2029    <tr class="shaded">
2030      <td>Raw bioassay A.24h (dye-swap)</td>
2031      <td>Generic/GenePix</td>
2032      <td>Scan A.24h (dye-swap)</td>
2033      <td>-</td>
2034      <td>Array design A</td>
2035      <td>Feature extraction A</td>
2036      <td>Software A</td>
2037      <td><i>Raw data</i>: <code>mouse/genepix.mouse.v4.37k.24h.dyeswap.gpr</code></td>
2038    </tr>
2039    <tr>
2040      <td>Affymetrix raw A.1</td>
2041      <td>Affymetrix</td>
2042      <td>Affymetrix scan A.1</td>
2043      <td>-</td>
2044      <td>Affymetrix A</td>
2045      <td>Feature extraction A</td>
2046      <td>Software A</td>
2047      <td><i>CEL file</i>: <code>affymetrix/E-TEST-1.ebi.ac.uk/jos1761.cel</code></td>
2048    </tr>   
2049    <tr>
2050      <td>Affymetrix raw A.2</td>
2051      <td>Affymetrix</td>
2052      <td>Affymetrix scan A.2</td>
2053      <td>-</td>
2054      <td>Affymetrix A</td>
2055      <td>Feature extraction A</td>
2056      <td>Software A</td>
2057      <td><i>CEL file</i>: <code>affymetrix/E-TEST-1.ebi.ac.uk/jos1762.cel</code></td>
2058    </tr>   
2059    <tr>
2060      <td>Affymetrix raw A.3</td>
2061      <td>Affymetrix</td>
2062      <td>Affymetrix scan A.3</td>
2063      <td>-</td>
2064      <td>Affymetrix A</td>
2065      <td>Feature extraction A</td>
2066      <td>Software A</td>
2067      <td><i>CEL file</i>: <code>affymetrix/E-TEST-1.ebi.ac.uk/jos1763.cel</code></td>
2068    </tr>   
2069    <tr class="shaded">
2070      <td>SeqRaw A.00h</td>
2071      <td>Sequencing/Expression-like/Cufflinks</td>
2072      <td>Arrangement A.00h</td>
2073      <td>Library A.00h</td>
2074      <td>RefSeqDesign A</td>
2075      <td>Cufflinks Settings A</td>
2076      <td>Cufflinks</td>
2077      <td><i>FPKM tracking file</i>: <code>sequencing/dataset1_norm1/isoforms.fpkm_tracking</code></td>
2078    </tr>
2079    <tr class="shaded">
2080      <td>SeqRaw A.24h</td>
2081      <td>Sequencing/Expression-like/Cufflinks</td>
2082      <td>Arrangement A.24h</td>
2083      <td>Library A.24h</td>
2084      <td>RefSeqDesign A</td>
2085      <td>Cufflinks Settings A</td>
2086      <td>Cufflinks</td>
2087      <td><i>FPKM tracking file</i>: <code>sequencing/dataset2_norm1/isoforms.fpkm_tracking</code></td>
2088    </tr>
2089    </table>
2090    <p>
2091  </li>
2092  </ol>
2093 
2094  <a name="step3"></a>
2095  <h3>Third step</h3>
2096  <ol>
2097  <li>
2098    Create experiments:
2099    <table class="listing" cellspacing="0" cellpadding="2" border="0">
2100    <tr>
2101      <th>Name</th>
2102      <th>Raw data type</th>
2103      <th>Raw bioassays</th>
2104      <th>Experimental factors</th>
2105    </tr>
2106    <tr>
2107      <td>Experiment A</td>
2108      <td>GenePix</td>
2109      <td>Raw bioassay A.00h,<br>Raw bioassay A.24h,<br>Raw bioassay A.00h (dye-swap),<br>
2110        Raw bioassay A.24h (dye-swap)</td>
2111      <td>Drug resistance, Time, RIN, Dye swap, PMT gain</td>
2112    </tr>
2113    <tr>
2114      <td>Affymetrix A</td>
2115      <td>Affymetrix</td>
2116      <td>Affymetrix raw A.1,<br>Affymetrix raw A.2,<br>Affymetrix raw A.3</td>
2117      <td>Drug resistance, Time, RIN, PMT gain</td>
2118    </tr>
2119    <tr>
2120      <td>Sequence A</td>
2121      <td>Cufflinks</td>
2122      <td>SeqRaw A.00h,<br>SeqRaw A.24h</td>
2123      <td>Drug resistance, Time, RIN</td>
2124    </tr>
2125    </table>
2126    <p>
2127  </li>
2128 
2129  <li>
2130    Import raw data to the Genepix and Cufflinks raw bioassays.
2131    There are two possible ways to do this:
2132    <ol>
2133    <li>Manually import to each raw bioassay.
2134    <li>Batch import to multiple raw bioassays.
2135    </ol>
2136    <p>
2137    <b>Manual import:</b> Go to the properties tab for each raw bioassay.
2138    Click on the <i>Import</i> button and use the auto-detect feature to
2139    import the raw data. Use the default configuration values except for
2140    those listed in the table below.
2141    <p>
2142   
2143    <b>Batch import:</b> The batch import is started from the
2144    properties tab of the <i>experiment</i>. Click on "Import" and
2145    use the auto-detect feature with one of the files from the raw bioassays.
2146    Use the default
2147    configuration values except for those listed in the table below.
2148    The batch import should import two raw data sets in one go (since it can
2149    only work with a single file format at a time and the dye-swap files uses
2150    a different file format). Repeat the batch import a second time to import
2151    the remaining two raw data sets.
2152    <p>
2153   
2154    <table class="listing" cellspacing="0" cellpadding="2" border="0">
2155    <tr>
2156      <th>Parameter</th>
2157      <th>Value</th>
2158      <th>Mode</th>
2159    </tr>
2160    <tr>
2161      <td>Feature mismatch</td>
2162      <td>smart</td>
2163      <td>both</td>
2164    </tr>
2165    <tr>
2166      <td>Invalid numeric value</td>
2167      <td>null</td>
2168      <td>both</td>
2169    </tr>
2170    <tr>
2171      <td>Log file</td>
2172      <td>~/import.log</td>
2173      <td>batch import</td>
2174    </tr>
2175    </table>
2176    <p>
2177       
2178    In both cases, the import should produce the same results
2179    as in the table below. When using the batch import mode, the
2180    detailed information for each raw bioassay is only found in
2181    the log file.
2182    <table class="listing" cellspacing="0" cellpadding="2" border="0">
2183    <tr>
2184      <th>Raw bioassay</th>
2185      <th>Raw data file</th>
2186      <th>Spots inserted/with null reporter/skipped)</th>
2187      <th>Annotations created</th>
2188    </tr>
2189    <tr>
2190      <td>Raw bioassay A.00h</td>
2191      <td>genepix.mouse.v4.37k.00h.gpr</td>
2192      <td>36,864/632/768</td>
2193      <td><i>Dye swap</i>: false</td>
2194    </tr>
2195    <tr>
2196      <td>Raw bioassay A.24h</td>
2197      <td>genepix.mouse.v4.37k.24h.gpr</td>
2198      <td>36,864/632/768</td>
2199      <td><i>Dye swap</i>: false</td>
2200    </tr>   
2201    <tr class="shaded">
2202      <td>Raw bioassay A.00h (dye-swap)</td>
2203      <td>genepix.mouse.v4.37k.00h.dyeswap.gpr</td>
2204      <td>36,864/632/768</td>
2205      <td><i>Dye swap</i>: true</td>
2206    </tr> 
2207    <tr class="shaded">
2208      <td>Raw bioassay A.24h (dye-swap)</td>
2209      <td>genepix.mouse.v4.37k.24h.dyeswap.gpr</td>
2210      <td>36,864/632/768</td>
2211      <td><i>Dye swap</i>: true</td>
2212    </tr>
2213    <tr>
2214      <td>SeqRaw A.00h</td>
2215      <td>dataset1_norm1/isoforms.fpkm_tracking</td>
2216      <td>38,293/0/0</td>
2217      <td>-</td>
2218    </tr>
2219    <tr>
2220      <td>SeqRaw A.24h</td>
2221      <td>dataset2_norm1/isoforms.fpkm_tracking</td>
2222      <td>38,293/0/0</td>
2223      <td>-</td>
2224    </tr>   
2225    </table>
2226    <p>
2227   
2228  </li>
2229 
2230  <li><a name="inheritannotations"></a>
2231    Inherit the annotations from the scans, extracts, samples and biosource for each root raw bioassay.
2232    Use the <i>auto-inherit</i> function that exists on the experiment properties
2233    tab. Make sure that all experimental factors are selected by the check boxes,
2234    then click on the <i>Auto-inherit</i> link in the column header. Use the <b>Inherit</b> 
2235    option for some annotations and <b>Clone</b> option for some. Uncheck the <b>No duplicates</b>
2236    option for the <i>RIN</i> annotation (see note 2 below).
2237    <br>
2238    <b>Note!</b> The <i>Affymetrix raw A.3</i>
2239    data set is missing biomaterial parents with annotations.<br>
2240    <b>Note 2!</b> In <i>Experiment A</i> there are duplicate values for the <i>RIN</i>
2241    annotations. Verify and fix this by manually removing the annotations that are inherited
2242    from the <i>Extract A.ref.qc</i> extract (value=9.2).
2243    <p>
2244
2245  </li>
2246 
2247 
2248  <li>
2249    Check the experiment overview page and use the <b>Validate</b> function
2250    for each of the three experiments.
2251    <p>
2252   
2253    It should display one warning for the <b>Experiment A</b> experiment. The warning is
2254    related to a missing biosurce on the reference sample.
2255    <p>
2256    The <b>Affymetrix A</b> experiment gives some more warnings. Most of them are
2257    related to not using the project default items, missing protocols
2258    and missing hardware. There should also be an error about missing
2259    experimental factor values for the <code>Affymetrix.3</code>
2260    raw bioassay. It is expected since this comes from the reference sample
2261    which doesn't have values for those annotations. The warnings about the
2262    number of spots mismatch is expected since the array design count probesets,
2263    while the raw bioassays count probes.
2264    <p>
2265   
2266    The <b>Sequence A</b> experiment also has some missing items, and a different
2267    raw data type for the experiment and raw bioassays.
2268   
2269    <p>
2270    Change validation options to reduce the number of warnings:
2271    <table class="listing" cellspacing="0" cellpadding="2" border="0">
2272    <tr>
2273      <th>Validation option</th>
2274      <th>Setting</th>
2275    </tr>
2276    <tr>
2277      <td>Project defaults</td>
2278      <td>Set all to <code>Ignore</code></td>
2279    </tr>
2280    <tr>
2281      <td>Missing items</td>
2282      <td>Set all to <code>Ignore</code></td>
2283    </tr>
2284    <tr>
2285      <td>Annotations - Missing factor value</td>
2286      <td><code>Warning</code></td>
2287    </tr>
2288    <tr>
2289      <td>Other - Raw spots &lt;&gt; features</td>
2290      <td><code>Ignore</code></td>
2291    </tr>
2292    </table>
2293   
2294    After the changes there should now only be two warnings about the
2295    missing factor values for the Affymetrix experiment and no warnings
2296    at all for the other experiments.
2297   
2298    <p>
2299  </li>
2300 
2301  </ol>
2302  </li>
2303  </ol>
2304
2305  <a name="analysis"></a>
2306  <h2>6. Analysis tests</h2>
2307  <p>
2308    Now it is time to analyse the data. The analysis test should be done
2309    by both a regular user and a guest.
2310  </p>
2311 
2312  <ol>
2313  <li>
2314    Activate the <code>Project A</code> project<p>
2315  </li>
2316   
2317  <li>
2318    Go to the <code>Experiment A</code> experiment.
2319    <p>
2320  </li>
2321 
2322  <li>
2323    Clone the reporters:
2324    <table class="listing" cellspacing="0" cellpadding="2" border="0">
2325    <tr>
2326      <th>Clone template</th>
2327      <th>Clone source</th>
2328    </tr>
2329    <tr>
2330      <td>Template A</td>
2331      <td>Raw data</td>
2332    </tr>
2333    </table>
2334    Click on "Next" and wait for the plug-in to finish. It should
2335    report that 35,912 reporters has been cloned.
2336    <p>
2337  </li>
2338 
2339  <li>
2340    Switch to the "Bioassay sets" tab. Create a new root bioassay set:
2341    <table class="listing" cellspacing="0" cellpadding="2" border="0">
2342    <tr>
2343      <th>Bioassay set name</th>
2344      <th>Raw bioassays</th>
2345      <th>Formula</th>
2346    </tr>
2347    <tr>
2348      <td>Root bioassay set</td>
2349      <td>all</td>
2350      <td>Mean FG - Mean BG</td>
2351    </tr>
2352    </table>
2353    Wait for the plug-in to finish.
2354    <p>
2355  </li>
2356 
2357  <li>
2358    Select the created bioassay set and create a filtered bioassayset:
2359    <table class="listing" cellspacing="0" cellpadding="2" border="0">
2360    <tr>
2361      <th>Child name</th>
2362      <th>Filter preset</th>
2363      <th>Expression</th>
2364    </tr>
2365    <tr>
2366      <td>Filtered bioassay set</td>
2367      <td>-</td>
2368      <td>ch(1) &gt; 0 &amp;&amp; ch(2) &gt; 0 &amp;&amp; rep('id') != null</td>
2369    </tr>
2370    </table>
2371    Wait for the plug-in to finish. It should report that 136,498 spots remain and
2372    that 10,958 spots has been removed.
2373    <p>
2374  </li>
2375
2376  <li>
2377    Select the filtered bioassay set and run a normalization plug-in:
2378    <table class="listing" cellspacing="0" cellpadding="2" border="0">
2379    <tr>
2380      <th>Plugin</th>
2381      <th>Parameters</th>
2382    </tr>
2383    <tr>
2384      <td>Normalization: Lowess</td>
2385      <td>Accept the default parameters.</td>
2386    </tr>
2387    </table>
2388    Wait for the plug in to finish. It should report that 136,498 spots has been
2389    normalized and 0 spots has been removed.
2390    <p>
2391  </li>
2392   
2393  <li>
2394    Select the normalized bioassay set and check the MA plots and
2395    the correction factor plots. Here are four examples:
2396    <table class="listing" cellspacing="0" cellpadding="2" border="0">
2397    <tr>
2398      <th>MA plots</th>
2399      <th>Correction factor plots</th>
2400    </tr>
2401    <tr>
2402      <td><img src="overview.png"><br><img src="overview.dyeswap.png"></td>
2403      <td><img src="correction.png"><br><img src="correction.dyeswap.png"></td>
2404    </tr>
2405    </table>
2406    <p>
2407  </li>
2408 
2409  <li>
2410    Try the plot tool with the following plots. Use the <code>Save</code> function
2411    to save one them as a file in the BASE file system, and the <code>Download</code> 
2412    function  to download a plot to your computer.
2413    <table class="listing" cellspacing="0" cellpadding="2" border="0">
2414    <tr>
2415      <th>Plot type</th>
2416      <th>Y-axis preset</th>
2417      <th>X-axis preset</th>
2418      <th>Other options</th>
2419    </tr>
2420    <tr>
2421      <td>Scatter plot</td>
2422      <td>M, log2(ch1 / ch2)</td>
2423      <td>A, log10(ch1 * ch2) / 2</td>
2424      <td>-</td>
2425    </tr>
2426    <tr>
2427      <td>Histogram plot</td>
2428      <td>Count</td>
2429      <td>Ratio, ch1 / ch2</td>
2430      <td>
2431        <table border="0" cellspacing="0" cellpadding="2">
2432        <tr>
2433          <td><i>Log scale</i></td>
2434          <td>checked</td>
2435        </tr>
2436        <tr>
2437          <td><i>Bin size</i></td>
2438          <td>0.1</td>
2439        </tr>
2440        <tr>
2441          <td><i>Annotation</i></td>
2442          <td>Time</td>
2443        </tr>
2444        </table>
2445      </td>
2446    </tr>
2447    </table>
2448    <p>
2449    Here are two examples:
2450    <table class="listing" cellspacing="0" cellpadding="2" border="0">
2451    <tr>
2452      <th>Scatter plot</th>
2453    </tr>
2454    <tr>
2455      <td><img src="scatter.png"></td>
2456    </tr>
2457    </table>
2458    <p>
2459    <table class="listing" cellspacing="0" cellpadding="2" border="0">
2460    <tr>
2461      <th>Histogram plot</th>
2462    </tr>
2463    <tr>
2464      <td><img src="histogram.png"></td>
2465    </tr>
2466    </table>
2467    <p>
2468  </li>
2469 
2470  </ol>
2471
2472
2473</body>
2474</html>
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