Context Navigation

index.html @ 5699

Visit:

Last change on this file since 5699 was 5699, checked in by Nicklas Nordborg, 12 years ago

References #1613: Extend the 'roles' test case with some sequence-related tests

Fixed in the manual test instructions and the hard-coded programmatic tests. The exception is that we do not yet have a defined raw data type + test data files for sequence data (using GenePix? as a temporary solution). The overview tests can't be completed until the item overview has been fixed by #1153.

The batch importer tests (instructions + programmatic tests) have not been fixed yet.

Property svn:eol-style set to native
Property svn:keywords set to Date Id

File size: 51.9 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 5699 2011-08-16 12:43:45Z 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: 2011-08-16 12:43:45 +0000 (Tue, 16 Aug 2011) $
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: hybridizations, scans, images, 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 2 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. These need to be uncompressed before they are uploaded to BASE.
150	</p>
151
152	<p>
153	To run the tests do the following:
154	</p>
155	<ol>
156
157	<li>Compile the core and the test programs: <code>ant main test</code>.</li>
158
159	<li>Change to the <code>build/test/</code> directory.</li>
160
161	<li>Run test programs: <code>./test.sh roles [OPTION] <cmds></code> where
162	<code><cmds></code> is one or more of the following:
163	<ul>
164	<li><code>all</code>: run all tests</li>
165	<li><code>root</code>: run the root user tests</li>
166	<li><code>admin</code>: run the administrator tests</li>
167	<li><code>power</code>: run the power user tests</li>
168	<li><code>user</code>: run the regular user tests</li>
169	<li><code>guest</code>: run the guest user tests</li>
170	</ul>
171	and <code>OPTION</code> can be none or more of:
172	<ul>
173	<li><code>-b</code>: if the batch importers should be tested</li>
174	<li><code>-w</code>: if the test program should wait for ENTER before emptying the database.</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>Array design importer</li>
290	<li>Array batch importer</li>
291	<li>Array slide importer</li>
292	</ul>
293	</td>
294	</tr>
295	</table>
296	<p>
297	</li>
298
299	<li>
300	Create file formats (<i>i.e.</i>, plug-in configurations) for importing
301	reporters. The formats marked as
302	optional are not used in the test procedure, but may be useful to weed
303	out import problems, since they allow importing all info from the raw
304	data files. You may either enter the regular expressions as specified or
305	use the "Test with file" feature.
306
307	<table class="listing" cellspacing="0" cellpadding="2" border="0">
308	<tr>
309	<th>Name</th>
310	<th>Plugin</th>
311	<th>Configuration values</th>
312	</tr>
313	<tr class="oddrow">
314	<td>Reporters for project A</td>
315	<td>Reporter importer</td>
316	<td>
317	<b>Test with file:</b> <code>plates_and_reporters.mouse.v4.37k.txt</code>
318	<table border="0" cellspacing="0" cellpadding="2">
319	<tr>
320	<td><i>Data header</i></td>
321	<td>384_number\t384_column\t384_row\t384_position\toligo_id.*</td>
322	</tr>
323	<tr>
324	<td><i>Data splitter</i></td>
325	<td>\t</td>
326	</tr>
327	<tr>
328	<td><i>Min data columns</i></td>
329	<td>5</td>
330	</tr>
331	<tr>
332	<td><i>Name</i></td>
333	<td>\oligo_id\</td>
334	</tr>
335	<tr>
336	<td><i>External ID</i></td>
337	<td>\oligo_id\</td>
338	</tr>
339	<tr>
340	<td><i>Description</i></td>
341	<td>\description_Ensembl*\</td>
342	</tr>
343	<tr>
344	<td><i>Gene symbol</i></td>
345	<td>\gene_symbol_Ensembl*\</td>
346	</tr>
347	<tr>
348	<td><i>Sequence</i></td>
349	<td>\oligo_sequence\</td>
350	</tr>
351	</table>
352
353	</td>
354	</tr>
355
356	<tr class="evenrow">
357	<td>GenePix reporter importer<br>(optional)</td>
358	<td>Reporter importer</td>
359	<td>
360
361	<b>Test with file:</b> <code>genepix.mouse.v4.37k.00h.gpr</code>
362	<table border="0" cellspacing="0" cellpadding="2">
363	<tr>
364	<td><i>Data header</i></td>
365	<td>"Block"\t"Column"\t"Row"\t"Name"\t"ID"\t.*</td>
366	</tr>
367	<tr>
368	<td><i>Data splitter</i></td>
369	<td>\t</td>
370	</tr>
371	<tr>
372	<td><i>Min data columns</i></td>
373	<td>48</td>
374	</tr>
375	<tr>
376	<td><i>Max data columns</i></td>
377	<td>48</td>
378	</tr>
379	<tr>
380	<td><i>Name</i></td>
381	<td>\Name\</td>
382	</tr>
383	<tr>
384	<td><i>External ID</i></td>
385	<td>\ID\</td>
386	</tr>
387	</table>
388
389	</td>
390	</tr>
391	<tr class="oddrow">
392	<td>Reporters from Affymetrix annotations file</td>
393	<td>Reporter importer</td>
394	<td>
395	<b>Test with file:</b> <code>MG_U74Av2_annot.csv.bz2</code>
396	<table border="0" cellspacing="0" cellpadding="2">
397	<tr>
398	<td><i>Data header</i></td>
399	<td>"Probe Set ID","GeneChip Array".*</td>
400	</tr>
401	<tr>
402	<td><i>Data splitter</i></td>
403	<td>(?!"),(?=")</td>
404	</tr>
405	<tr>
406	<td><i>Name</i></td>
407	<td>\Probe Set ID\</td>
408	</tr>
409	<tr>
410	<td><i>External ID</i></td>
411	<td>\Probe Set ID\</td>
412	</tr>
413	<tr>
414	<td><i>Description</i></td>
415	<td>\Target Description\</td>
416	</tr>
417	<tr>
418	<td><i>Gene symbol</i></td>
419	<td>\Gene Symbol\</td>
420	</tr>
421	</table>
422
423	</td>
424	</tr>
425	</table>
426	<p>
427	</li>
428
429	<li>
430	Import reporters:
431	<ol>
432	<li>Go to the <code>View -> Reporters</code> page.</li>
433	<li>Click on the <code>Import</code> button.</li>
434	<li>Choose <code>auto-detect</code> and then upload
435	the file <code>plates_and_reporters.mouse.v4.37k.txt</code>.</li>
436	<li>The <code>Reporters for project A</code> format should be
437	found.</li>
438	<li>Select the <code>skip</code> option for the "Missing a required" value
439	since the file contains rows with empty reporter ID:s.
440	<li>Continue and wait for the import to finish. It should create 35,912 new reporters.</li>
441	<li>
442	Repeat the procedure with the <code>MG_U74Av2_annot.csv</code> file. This time
443	also select <code>crop</code> for the "String too long" setting since
444	the file contains data that is too large for the datbase.
445	12,488 new reporters should be created.
446	</ol>
447	<p>
448
449	</li>
450
451
452	</ol>
453
454
455	<a name="power"></a>
456	<h2>4. Power user tests</h2>
457	<p>
458	The power user is the typical owner/administrator of a project. The power user sets
459	up common resources used in the project, such as hardware, software, protocols,
460	file formats and annotation types. In this case the power user is also responsible for
461	managing the LIMS.
462	</p>
463
464	<ol>
465	<li>
466	Create a project:
467
468	<table class="listing" cellspacing="0" cellpadding="2" border="0">
469	<tr>
470	<th>Name</th>
471	<th>Members</th>
472	</tr>
473	<tr>
474	<td>Project A</td>
475	<td>Groups: Group A (Use permission)</td>
476	</tr>
477	</table>
478	<p>
479	</li>
480
481	<li>Activate the project.<p></li>
482
483	<li>
484	Create annotation types [A] and protocol parameters [P]:
485	<table class="listing" cellspacing="0" cellpadding="2" border="0">
486	<tr>
487	<th>Name</th>
488	<th>Type</th>
489	<th>Unit</th>
490	<th>Interface</th>
491	<th>Values</th>
492	<th>Item types</th>
493	</tr>
494	<tr>
495	<td>Drug resistance [A]</td>
496	<td>String</td>
497	<td>-</td>
498	<td>radiobuttons</td>
499	<td>high, medium, low</td>
500	<td>Biosource</td>
501	</tr>
502	<tr>
503	<td>Time [A]</td>
504	<td>Integer</td>
505	<td>Hour</td>
506	<td>text box</td>
507	<td>-</td>
508	<td>Sample</td>
509	</tr>
510	<tr>
511	<td>Dye swap [A]</td>
512	<td>Boolean</td>
513	<td>-</td>
514	<td>-</td>
515	<td>-</td>
516	<td>Raw bioassay</td>
517	</tr>
518	<tr>
519	<td>PMT gain [P]</td>
520	<td>Float</td>
521	<td>Volt (Electric potential)</td>
522	<td>-</td>
523	<td>-</td>
524	<td>Scan</td>
525	</tr>
526	</table>
527	<p>
528	</li>
529
530	<li>
531	Create protocols:
532	<table class="listing" cellspacing="0" cellpadding="2" border="0">
533	<tr>
534	<th>Name</th>
535	<th>Type</th>
536	<th>Comment</th>
537	</tr>
538	<tr>
539	<td>Sampling A</td>
540	<td>Sampling</td>
541	</tr>
542	<tr>
543	<td>Extraction A</td>
544	<td>Extraction</td>
545	</tr>
546	<tr>
547	<td>Labeling A</td>
548	<td>Labeling</td>
549	</tr>
550	<tr>
551	<td>Library preparation A</td>
552	<td>Library preparation</td>
553	</tr>
554	<tr>
555	<td>Hybridization A</td>
556	<td>Hybridization</td>
557	</tr>
558	<tr>
559	<td>cBot Settings A</td>
560	<td>Cluster generation</td>
561	</tr>
562	<tr>
563	<td>Scanning A</td>
564	<td>Scanning</td>
565	<td>Select 'PMT gain' as a protocol parameter.</td>
566	</tr>
567	<tr>
568	<td>HiSeq Settings A</td>
569	<td>Sequencing</td>
570	</tr>
571	<tr>
572	<td>TopHat Settings A</td>
573	<td>Alignment</td>
574	</tr>
575	<tr>
576	<td>Feature extraction A</td>
577	<td>Feature extraction</td>
578	</tr>
579	<tr>
580	<td>Cufflinks Settings A</td>
581	<td>Feature extraction</td>
582	</tr>
583	<tr>
584	<td>Printing A</td>
585	<td>Printing</td>
586	</tr>
587	</table>
588	<p>
589	</li>
590
591	<li>
592	Create hardware:
593	<table class="listing" cellspacing="0" cellpadding="2" border="0">
594	<tr>
595	<th>Name</th>
596	<th>Type</th>
597	</tr>
598	<tr>
599	<td>Hybridization station A</td>
600	<td>Hybridization station</td>
601	</tr>
602	<tr>
603	<td>cBot A</td>
604	<td>Cluster generator</td>
605	</tr>
606	<tr>
607	<td>HiSeq 2000 A</td>
608	<td>Sequencer</td>
609	</tr>
610	<tr>
611	<td>Scanner A</td>
612	<td>Scanner</td>
613	</tr>
614	<tr>
615	<td>Print robot A</td>
616	<td>Print robot</td>
617	</tr>
618	</table>
619	<p>
620	</li>
621
622	<li>
623	Create software:
624	<table class="listing" cellspacing="0" cellpadding="2" border="0">
625	<tr>
626	<th>Name</th>
627	<th>Type</th>
628	</tr>
629	<tr>
630	<td>Software A</td>
631	<td>Feature extraction</td>
632	</tr>
633	</table>
634	<p>
635	</li>
636
637	<li>
638	Create bioplate type:
639	<table class="listing" cellspacing="0" cellpadding="2" border="0">
640	<tr>
641	<th>Name</th>
642	<th>Biomaterial type</th>
643	<th>Well lock mode</th>
644	</tr>
645	<tr>
646	<td>Bioplate type A</td>
647	<td>Any</td>
648	<td>Unlocked</td>
649	</tr>
650	</table>
651	<p>
652	</li>
653
654	<li>
655	Create file formats (<i>i.e.</i>, plug-in configurations). The formats marked as
656	optional are not used in the test procedure, but may be useful to weed
657	out import problems, since they allow importing all info from the raw
658	data files. You may either enter the regular expressions as specified or
659	use the "Test with file" feature.
660
661	<table class="listing" cellspacing="0" cellpadding="2" border="0">
662	<tr>
663	<th>Name</th>
664	<th>Plugin</th>
665	<th>Configuration values</th>
666	</tr>
667
668	<tr class="oddrow">
669	<td>Plates for project A</td>
670	<td>Plate importer</td>
671	<td>
672
673	<b>Test with file:</b> <code>plates_and_reporters.mouse.v4.37k.txt</code>
674	<table border="0" cellspacing="0" cellpadding="2">
675	<tr>
676	<td><i>Data header</i></td>
677	<td>384_number\t384_column\t384_row\t384_position\toligo_id.*</td>
678	</tr>
679	<tr>
680	<td><i>Data splitter</i></td>
681	<td>\t</td>
682	</tr>
683	<tr>
684	<td><i>Min data columns</i></td>
685	<td>5</td>
686	</tr>
687	<tr>
688	<td><i>Plate number/name</i></td>
689	<td>\384_number\</td>
690	</tr>
691	<tr>
692	<td><i>Row</i></td>
693	<td>\384_row\</td>
694	</tr>
695	<tr>
696	<td><i>Column</i></td>
697	<td>\384_column\</td>
698	</tr>
699	<tr>
700	<td><i>Reporter ID</i></td>
701	<td>\oligo_id\</td>
702	</tr>
703	</table>
704
705	</td>
706	</tr>
707
708	<tr class="evenrow">
709	<td>GenePix feature importer<br>(optional)</td>
710	<td>Reporter map importer</td>
711	<td>
712
713	<b>Test with file:</b> <code>genepix.mouse.v4.37k.00h.gpr</code>
714	<table border="0" cellspacing="0" cellpadding="2">
715	<tr>
716	<td><i>Data header</i></td>
717	<td>"Block"\t"Column"\t"Row"\t"Name"\t"ID"\t.*</td>
718	</tr>
719	<tr>
720	<td><i>Data splitter</i></td>
721	<td>\t</td>
722	</tr>
723	<tr>
724	<td><i>Min data columns</i></td>
725	<td>48</td>
726	</tr>
727	<tr>
728	<td><i>Max data columns</i></td>
729	<td>48</td>
730	</tr>
731	<tr>
732	<td><i>Reporter ID</i></td>
733	<td>\ID\</td>
734	</tr>
735	<tr>
736	<td><i>Block</i></td>
737	<td>\Block\</td>
738	</tr>
739	<tr>
740	<td><i>Column</i></td>
741	<td>\Column\</td>
742	</tr>
743	<tr>
744	<td><i>Row</i></td>
745	<td>\Row\</td>
746	</tr>
747	</table>
748
749	</td>
750	</tr>
751
752	<tr class="oddrow">
753	<td>Raw data for project A</td>
754	<td>Raw data importer</td>
755	<td>
756
757	<b>Test with file:</b> <code>genepix.mouse.v4.37k.00h.gpr</code>
758	<table border="0" cellspacing="0" cellpadding="2">
759	<tr>
760	<td><i>Raw data type</i></td>
761	<td>Genepix</td>
762	</tr>
763	<tr>
764	<td><i>Header</i></td>
765	<td>"(.+)=(.*)"</td>
766	</tr>
767	<tr>
768	<td><i>Data header</i></td>
769	<td>"Block"\t"Column"\t"Row"\t"Name"\t"ID"\t."Ratio of Medians $532\/635$".</td>
770	</tr>
771	<tr>
772	<td><i>Data splitter</i></td>
773	<td>\t</td>
774	</tr>
775	<tr>
776	<td><i>Min data columns</i></td>
777	<td>48</td>
778	</tr>
779	<tr>
780	<td><i>Max data columns</i></td>
781	<td>48</td>
782	</tr>
783
784	<tr>
785	<td><i>Block</i></td>
786	<td>\Block\</td>
787	</tr>
788	<tr>
789	<td><i>Column</i></td>
790	<td>\Column\</td>
791	</tr>
792	<tr>
793	<td><i>Row</i></td>
794	<td>\Row\</td>
795	</tr>
796	<tr>
797	<td><i>X</i></td>
798	<td>\X\</td>
799	</tr>
800	<tr>
801	<td><i>Y</i></td>
802	<td>\Y\</td>
803	</tr>
804	<tr>
805	<td><i>Reporter ID</i></td>
806	<td>\ID\</td>
807	</tr>
808	<tr>
809	<td><i>Spot diameter</i></td>
810	<td>\Dia.\</td>
811	</tr>
812	<tr>
813	<td><i>Channel 1 foreground median</i></td>
814	<td>\F635 Median\</td>
815	</tr>
816	<tr>
817	<td><i>Channel 1 foreground mean</i></td>
818	<td>\F635 Mean\</td>
819	</tr>
820	<tr>
821	<td><i>Channel 1 foreground standard deviation</i></td>
822	<td>\F635 SD\</td>
823	</tr>
824	<tr>
825	<td><i>Channel 1 background median</i></td>
826	<td>\B635 Median\</td>
827	</tr>
828	<tr>
829	<td><i>Channel 1 background mean</i></td>
830	<td>\B635 Mean\</td>
831	</tr>
832	<tr>
833	<td><i>Channel 1 background standard deviation</i></td>
834	<td>\B635 SD\</td>
835	</tr>
836	<tr>
837	<td><i>Percent pixels within 1 standard deviation</i></td>
838	<td>\% > B635+1SD\</td>
839	</tr>
840	<tr>
841	<td><i>Percent pixels within 2 standard deviations</i></td>
842	<td>\% > B635+2SD\</td>
843	</tr>
844	<tr>
845	<td><i>Percent saturated pixels</i></td>
846	<td>\F635 % Sat.\</td>
847	</tr>
848	<tr>
849	<td><i>Channel 2 foreground median</i></td>
850	<td>\F532 Median\</td>
851	</tr>
852	<tr>
853	<td><i>Channel 2 foreground mean</i></td>
854	<td>\F532 Mean\</td>
855	</tr>
856	<tr>
857	<td><i>Channel 2 foreground standard deviation</i></td>
858	<td>\F532 SD\</td>
859	</tr>
860	<tr>
861	<td><i>Channel 2 background median</i></td>
862	<td>\B532 Median\</td>
863	</tr>
864	<tr>
865	<td><i>Channel 2 background mean</i></td>
866	<td>\B532 Mean\</td>
867	</tr>
868	<tr>
869	<td><i>Channel 2 background standard deviation</i></td>
870	<td>\B532 SD\</td>
871	</tr>
872	<tr>
873	<td><i>Percent pixels within 1 standard deviation</i></td>
874	<td>\% > B532+1SD\</td>
875	</tr>
876	<tr>
877	<td><i>Percent pixels within 2 standard deviations</i></td>
878	<td>\% > B532+2SD\</td>
879	</tr>
880	<tr>
881	<td><i>Percent saturated pixels</i></td>
882	<td>\F532 % Sat.\</td>
883	</tr>
884	<tr>
885	<td><i>Foreground pixels</i></td>
886	<td>\F Pixels\</td>
887	</tr>
888	<tr>
889	<td><i>Background pixels</i></td>
890	<td>\B Pixels\</td>
891	</tr>
892	<tr>
893	<td><i>Flags</i></td>
894	<td>\Flags\</td>
895	</tr>
896	</table>
897
898	</td>
899	</tr>
900
901	<tr class="evenrow">
902	<td>Raw data for project A (dye-swap)</td>
903	<td>Raw data importer</td>
904	<td>
905
906	<b>Test with file:</b> <code>genepix.mouse.v4.37k.00h.dyeswap.gpr</code>
907	<table border="0" cellspacing="0" cellpadding="2">
908	<tr>
909	<td><i>Raw data type</i></td>
910	<td>Genepix</td>
911	</tr>
912	<tr>
913	<td><i>Header</i></td>
914	<td>"(.+)=(.*)"</td>
915	</tr>
916	<tr>
917	<td><i>Data header</i></td>
918	<td>"Block"\t"Column"\t"Row"\t"Name"\t"ID"\t."Ratio of Medians $635\/532$".</td>
919	</tr>
920	<tr>
921	<td><i>Data splitter</i></td>
922	<td>\t</td>
923	</tr>
924	<tr>
925	<td><i>Min data columns</i></td>
926	<td>48</td>
927	</tr>
928	<tr>
929	<td><i>Max data columns</i></td>
930	<td>48</td>
931	</tr>
932
933	<tr>
934	<td><i>Block</i></td>
935	<td>\Block\</td>
936	</tr>
937	<tr>
938	<td><i>Column</i></td>
939	<td>\Column\</td>
940	</tr>
941	<tr>
942	<td><i>Row</i></td>
943	<td>\Row\</td>
944	</tr>
945	<tr>
946	<td><i>X</i></td>
947	<td>\X\</td>
948	</tr>
949	<tr>
950	<td><i>Y</i></td>
951	<td>\Y\</td>
952	</tr>
953	<tr>
954	<td><i>Reporter ID</i></td>
955	<td>\ID\</td>
956	</tr>
957	<tr>
958	<td><i>Spot diameter</i></td>
959	<td>\Dia.\</td>
960	</tr>
961	<tr>
962	<td><i>Channel 1 foreground median</i></td>
963	<td>\F532 Median\</td>
964	</tr>
965	<tr>
966	<td><i>Channel 1 foreground mean</i></td>
967	<td>\F532 Mean\</td>
968	</tr>
969	<tr>
970	<td><i>Channel 1 foreground standard deviation</i></td>
971	<td>\F532 SD\</td>
972	</tr>
973	<tr>
974	<td><i>Channel 1 background median</i></td>
975	<td>\B532 Median\</td>
976	</tr>
977	<tr>
978	<td><i>Channel 1 background mean</i></td>
979	<td>\B532 Mean\</td>
980	</tr>
981	<tr>
982	<td><i>Channel 1 background standard deviation</i></td>
983	<td>\B532 SD\</td>
984	</tr>
985	<tr>
986	<td><i>Percent pixels within 1 standard deviation</i></td>
987	<td>\% > B532+1SD\</td>
988	</tr>
989	<tr>
990	<td><i>Percent pixels within 2 standard deviations</i></td>
991	<td>\% > B532+2SD\</td>
992	</tr>
993	<tr>
994	<td><i>Percent saturated pixels</i></td>
995	<td>\F532 % Sat.\</td>
996	</tr>
997	<tr>
998	<td><i>Channel 2 foreground median</i></td>
999	<td>\F635 Median\</td>
1000	</tr>
1001	<tr>
1002	<td><i>Channel 2 foreground mean</i></td>
1003	<td>\F635 Mean\</td>
1004	</tr>
1005	<tr>
1006	<td><i>Channel 2 foreground standard deviation</i></td>
1007	<td>\F635 SD\</td>
1008	</tr>
1009	<tr>
1010	<td><i>Channel 2 background median</i></td>
1011	<td>\B635 Median\</td>
1012	</tr>
1013	<tr>
1014	<td><i>Channel 2 background mean</i></td>
1015	<td>\B635 Mean\</td>
1016	</tr>
1017	<tr>
1018	<td><i>Channel 2 background standard deviation</i></td>
1019	<td>\B635 SD\</td>
1020	</tr>
1021	<tr>
1022	<td><i>Percent pixels within 1 standard deviation</i></td>
1023	<td>\% > B635+1SD\</td>
1024	</tr>
1025	<tr>
1026	<td><i>Percent pixels within 2 standard deviations</i></td>
1027	<td>\% > B635+2SD\</td>
1028	</tr>
1029	<tr>
1030	<td><i>Percent saturated pixels</i></td>
1031	<td>\F635 % Sat.\</td>
1032	</tr>
1033	<tr>
1034	<td><i>Foreground pixels</i></td>
1035	<td>\F Pixels\</td>
1036	</tr>
1037	<tr>
1038	<td><i>Background pixels</i></td>
1039	<td>\B Pixels\</td>
1040	</tr>
1041	<tr>
1042	<td><i>Flags</i></td>
1043	<td>\Flags\</td>
1044	</tr>
1045	</table>
1046
1047	</td>
1048	</tr>
1049	</table>
1050	<p>
1051	</li>
1052
1053	<li>
1054	Annotate the file formats:
1055	<table class="listing" cellspacing="0" cellpadding="2" border="0">
1056	<tr>
1057	<th>File format</th>
1058	<th>Annotation</th>
1059	<th>Value</th>
1060	</tr>
1061	<tr>
1062	<td>Raw data for project A</td>
1063	<td>Dye swap</td>
1064	<td>false</td>
1065	</tr>
1066	<tr>
1067	<td>Raw data for project A (dye swap)</td>
1068	<td>Dye swap</td>
1069	<td>true</td>
1070	</tr>
1071	</table>
1072	This will make the raw data importer automatically annotate the
1073	raw bioassays with the specified annotations.
1074	<p>
1075	</li>
1076
1077	<li>
1078	Create plate type:
1079	<table class="listing" cellspacing="0" cellpadding="2" border="0">
1080	<tr>
1081	<th>Name</th>
1082	<th>Geometry</th>
1083	</tr>
1084	<tr>
1085	<td>Plate type A</td>
1086	<td>384-well (16 x 24)</td>
1087	</tr>
1088	</table>
1089	<p>
1090	</li>
1091
1092	<li>
1093	Import plates:
1094	<ol>
1095	<li>Go to the <code>Array LIMS -> Plates</code> page.</li>
1096	<li>Click on the <code>Import</code> button.</li>
1097	<li>Choose <code>auto-detect</code> and select
1098	the file <code>plates_and_reporters.mouse.v4.37k.txt</code>.</li>
1099	<li>The <code>Plates for project A</code> format should be
1100	found.</li>
1101	<li>Specify the following parameters:
1102
1103	<table border="0" cellspacing="0" cellpadding="2">
1104	<tr>
1105	<td><i>Plate type</i></td>
1106	<td>Plate type A</td>
1107	</tr>
1108	<tr>
1109	<td><i>Plate name prefix</i></td>
1110	<td>Plate A</td>
1111	</tr>
1112	<tr>
1113	<td><i>Plate name padding</i></td>
1114	<td>4</td>
1115	</tr>
1116	</table>
1117	</li>
1118	<li>Continue and wait for the import to finish. It should create 96 plates.</li>
1119	</ol>
1120	<p>
1121	</li>
1122
1123	<li>
1124	Create array designs and upload data files to them:
1125	<table class="listing" cellspacing="0" cellpadding="2" border="0">
1126	<tr>
1127	<th>Name</th>
1128	<th>Platform</th>
1129	<th>File(s)</th>
1130	</tr>
1131	<tr>
1132	<td>Array design A</td>
1133	<td>Generic</td>
1134	<td><i>Print map</i>: printmap.mouse.v4.37k.tam</td>
1135	</tr>
1136	<tr>
1137	<td>Affymetrix A</td>
1138	<td>Affymetrix</td>
1139	<td><i>CDF file</i>: MG_U74Av2.cdf.bz2</td>
1140	</tr>
1141	</table>
1142	<p>
1143	Or
1144	<p>
1145	Import array designs with the ArrayDesignImporter plug-in.
1146	<ol>
1147	<li>Make sure the data-files, mentioned in table above, are located in <code>/home/power/</code>, upload them if not</li>
1148	<li>Click on the <code>Import</code> button on the array design list page.</li>
1149	<li>Choose ArrayDesignImporter in the plug-in drop-down list.</li>
1150	<li><b>Test with file:</b> <code>arraydesign_out.txt</code> and set
1151	the parsing parameters with help of the <code>Auto generate</code> button on the <code>Column mapping</code>
1152	tab.</li>
1153	<li>Start the import-job by clicking on the <code>Finish</code> button on the third wizard-page.</li>
1154	</ol>
1155	<p>
1156	</li>
1157
1158	<li>
1159	Connect <code>Array design A</code> with plates. Select the imported plates (plate names starting
1160	with <code>Plate A</code>) and sort them in the correct order (as indicated by their names).
1161	<p>
1162	</li>
1163
1164	<li>
1165	Import features:
1166	<ol>
1167	<li>Click on the <code>Import</code> button when viewing properties for the array design.</li>
1168	<li>Choose <code>auto-detect</code> and upload the file
1169	<code>printmap.mouse.v4.37k.tam</code>.</li>
1170	<li>The <code>Print map importer</code> plug-in should be
1171	found.</li>
1172	<li>Continue and wait for the import to finish. It should create 36,864 features and 48 blocks.</li>
1173	</ol>
1174	<p>
1175	</li>
1176
1177	<li>
1178	Set project defaults. Go to the projects page and edit the
1179	<code>Project A</code> project. On the <code>Defaults</code>
1180	tab, set the following defaults:
1181
1182	<table class="listing" cellspacing="0" cellpadding="2" border="0">
1183	<tr>
1184	<th>Setting</th>
1185	<th>Value(s)</th>
1186	</tr>
1187	<tr>
1188	<td>Raw data type</td>
1189	<td>Genepix</td>
1190	</tr>
1191	<tr>
1192	<td>Platforms</td>
1193	<td>
1194	Generic<br>
1195	Affymetrix
1196	</td>
1197	</tr>
1198	<tr>
1199	<td>Array designs</td>
1200	<td>
1201	Array design A<br>
1202	Affymetrix A
1203	</td>
1204	</tr>
1205	<tr>
1206	<td>Protocols</td>
1207	<td>
1208	Sampling A<br>
1209	Extraction A<br>
1210	Labeling A<br>
1211	Library preparation A<br>
1212	Hybridization A<br>
1213	cBot Settings A<br>
1214	Scanning A<br>
1215	HiSeq Settings A<br>
1216	TopHat Settings A<br>
1217	Feature extraction A<br>
1218	Cufflinks Settings A<br>
1219	Printing A
1220	</td>
1221	</tr>
1222	<tr>
1223	<td>Hardware</td>
1224	<td>
1225	Hybridization station A<br>
1226	cBot A<br>
1227	HiSeq 2000 A<br>
1228	Scanner A<br>
1229	Print robot A
1230	</td>
1231	</tr>
1232	<tr>
1233	<td>Software</td>
1234	<td>
1235	Software A<br>
1236	TopHat<br>
1237	Cufflinks
1238	</td>
1239	</tr>
1240	</table>
1241
1242	<p>
1243	</li>
1244
1245	<li>
1246	Create array batches:
1247	<table class="listing" cellspacing="0" cellpadding="2" border="0">
1248	<tr>
1249	<th>Name</th>
1250	<th>Array design</th>
1251	<th>Print robot</th>
1252	<th>Protocol</th>
1253	</tr>
1254	<tr>
1255	<td>Array batch A</td>
1256	<td>Array design A</td>
1257	<td>Robot A</td>
1258	<td>Printing A</td>
1259	</tr>
1260	<tr>
1261	<td>Affymetrix batch A</td>
1262	<td>Affymetrix A</td>
1263	<td></td>
1264	<td></td>
1265	</tr>
1266	</table>
1267	<p>
1268	Or
1269	<p>
1270	Import array batches with the ArrayBatchImporter plug-in.
1271	<ol>
1272	<li>Click on the <code>Import</code> button on the array batch list page.</li>
1273	<li>Select ArrayBatchImporter in the plug-in drop-down list and click <code>Next</code></li>
1274	<li><b>Test with file:</b> <code>arraybatch_out.txt</code> and set the parsing parameters
1275	with help of the <code>Auto generate</code> button on the <code>Column mapping</code>
1276	tab.</li>
1277	<li>Start the import-job by clicking on the <code>Finish</code> button on the third wizzard-page.</li>
1278	</ol>
1279	<p>
1280	</li>
1281
1282	<li>
1283	Create array slides with the <code>Create slides</code>
1284	wizard.
1285
1286	<table class="listing" cellspacing="0" cellpadding="2" border="0">
1287	<tr>
1288	<th>Name</th>
1289	<th>Array batch</th>
1290	<th>Quantity</th>
1291	</tr>
1292	<tr>
1293	<td>Array slide A.</td>
1294	<td>Array batch A</td>
1295	<td>4</td>
1296	</tr>
1297	<tr>
1298	<td>Affymetrix slide A.</td>
1299	<td>Affymetrix batch A</td>
1300	<td>3</td>
1301	</tr>
1302	</table>
1303	<p>
1304	Or
1305	<p>
1306	Import array slides with the ArraySlideImporter plug-in.
1307	<ol>
1308	<li>Click on the <code>Import</code> button on the array slide list page.</li>
1309	<li>Select ArraySlideImporter in the plug-in drop-down list and click <code>Next</code></li>
1310	<li><b>Test with file:</b> <code>arrayslide_out.txt</code> and set the parsing parameters
1311	with help of the <code>Auto generate</code> button on the <code>Column mapping</code>
1312	tab.</li>
1313	<li>Start the import-job by clicking on the <code>Finish</code> button on the third wizzard-page.</li>
1314	</ol>
1315	<p>
1316	</li>
1317	</ol>
1318
1319	<a name="user"></a>
1320	<h2>5. User tests</h2>
1321	<p>
1322	The user is a typical worker in the project. The user does the actual experimentation in the
1323	lab, which includes collecting samples, doing extraction, labeling and hybridizations.
1324	The user also scans and analyses the raw data resulting from the images. Inserting items can be
1325	done in two different ways, .
1326	</p>
1327	<h3>First step</h3>
1328
1329	<ol>
1330	<li>Activate the <code>Project A</code> project.
1331	<p>
1332
1333	<li>
1334	Create a bioplate:
1335	<table class="listing" cellspacing="0" cellpadding="2" border="0">
1336	<tr>
1337	<th>Name</th>
1338	<th>Plate geometry</th>
1339	<th>Bioplate type</th>
1340	</tr>
1341	<tr>
1342	<td>Bioplate A</td>
1343	<td>96-well (8 x 12)</td>
1344	<td>BioPlate type A</td>
1345	</tr>
1346	</table>
1347	<p>
1348	<li>Continue with the second step, which can be done with batch importers or
1349	manually.
1350
1351	</ol>
1352
1353
1354	<h3>Second step (using batch importers)</h3>
1355
1356	<ol>
1357	<li>Click on the <code>Import</code> button on the list page.</li>
1358	<li>Select <itemtype>Importer in the plug-in drop-down list and click <code>Next</code></li>
1359	<li><b>Test with file:</b> using the right file(listed below) and set the parsing parameters
1360	by using the <code>Auto generate</code> button on the <code>Column mapping</code> tab.
1361	<table class="listing" cellspacing="0" cellpadding="2" border="0">
1362	<tr>
1363	<th>Itemtype</th>
1364	<th>File</th>
1365	</tr>
1366	<tr>
1367	<td>Biosource</td>
1368	<td>biosource_out.txt</td>
1369	</tr>
1370	<tr>
1371	<td>Samples</td>
1372	<td>sample_out.txt</td>
1373	</tr>
1374	<tr>
1375	<td>Extracts</td>
1376	<td>extract_out.txt</td>
1377	</tr>
1378	<tr>
1379	<td>Labeled extracts</td>
1380	<td>labeledextract_out.txt</td>
1381	</tr>
1382	<tr>
1383	<td>Hybridizations</td>
1384	<td>hybridization_out.txt</td>
1385	</tr>
1386	<tr>
1387	<td>Scans</td>
1388	<td>scan_out.txt</td>
1389	</tr>
1390	<tr>
1391	<td>Raw bioassays</td>
1392	<td>rawbioassay_out.txt</td>
1393	</tr>
1394	</table>
1395	The files listed for biosource, samples and scans also contains annotations
1396	for the items and these files should also be used with the annotation importer.
1397	The procedure is the same as for batch importers except that only <code>\Name\</code>
1398	is needed in the column mapping. The annotation column should be selected by default in
1399	the second wizzard-step.
1400	</li>
1401	<li>Start the import-job by clicking on the <code>Finish</code> button on the third wizzard-page.</li>
1402	<li>Continue with <a href="#step3">the third step</a>.</li>
1403	</ol>
1404
1405	<h3>Second step (create items manually)</h3>
1406	<ol>
1407	<li>
1408	Create a biosource:
1409	<table class="listing" cellspacing="0" cellpadding="2" border="0">
1410	<tr>
1411	<th>Name</th>
1412	<th>Annotations</th>
1413	</tr>
1414	<tr>
1415	<td>Biosource A</td>
1416	<td>
1417	<table border="0" cellspacing="0" cellpadding="2">
1418	<tr>
1419	<td><i>Drug resistance:</i></td>
1420	<td>medium</td>
1421	</tr>
1422	</table>
1423	</td>
1424	</tr>
1425	</table>
1426	<p>
1427	</li>
1428
1429	<li>
1430	Create samples:
1431	<table class="listing" cellspacing="0" cellpadding="2" border="0">
1432	<tr>
1433	<th>Name</th>
1434	<th>Protocol</th>
1435	<th>Biosource</th>
1436	<th>Bioplate [well]</th>
1437	<th>Annotations</th>
1438	</tr>
1439	<tr>
1440	<td>Sample A.00h</td>
1441	<td>Sampling A</td>
1442	<td>Biosource A</td>
1443	<td>Bioplate A [A1]</td>
1444	<td>
1445	<table border="0" cellspacing="0" cellpadding="2">
1446	<tr>
1447	<td><i>Time:</i></td>
1448	<td>0h</td>
1449	</tr>
1450	</table>
1451	</td>
1452	</tr>
1453	<tr>
1454	<td>Sample A.24h</td>
1455	<td>Sampling A</td>
1456	<td>Biosource A</td>
1457	<td>Bioplate A [A2]</td>
1458	<td>
1459	<table border="0" cellspacing="0" cellpadding="2">
1460	<tr>
1461	<td><i>Time:</i></td>
1462	<td>24h</td>
1463	</tr>
1464	</table>
1465	</td>
1466	</tr>
1467	<tr>
1468	<td>Sample A.ref</td>
1469	<td>Sampling A</td>
1470	<td>-</td>
1471	<td>Bioplate A [A3]</td>
1472	<td>-</td>
1473	</tr>
1474	</table>
1475	<p>
1476	</li>
1477
1478	<li>
1479	Create extracts:
1480	<table class="listing" cellspacing="0" cellpadding="2" border="0">
1481	<tr>
1482	<th>Name</th>
1483	<th>Protocol</th>
1484	<th>Sample</th>
1485	<th>Bioplate [well]</th>
1486	</tr>
1487	<tr>
1488	<td>Extract A.00h</td>
1489	<td>Extraction A</td>
1490	<td>Sample A.00h</td>
1491	<td>Bioplate A [B1]</td>
1492	</tr>
1493	<tr>
1494	<td>Extract A.24h</td>
1495	<td>Extraction A</td>
1496	<td>Sample A.24h</td>
1497	<td>Bioplate A [B2]</td>
1498	</tr>
1499	<tr>
1500	<td>Extract A.ref</td>
1501	<td>Extraction A</td>
1502	<td>Sample A.ref</td>
1503	<td>Bioplate A [B3]</td>
1504	</tr>
1505	</table>
1506	<p>
1507	</li>
1508
1509	<li>
1510	Create labeled extracts and libraries:
1511	<table class="listing" cellspacing="0" cellpadding="2" border="0">
1512	<tr>
1513	<th>Name</th>
1514	<th>Label</th>
1515	<th>Protocol</th>
1516	<th>Extract</th>
1517	<th>Bioplate [well]</th>
1518	</tr>
1519	<tr>
1520	<td>Labeled extract A.00h</td>
1521	<td>cy3</td>
1522	<td>Labeling A</td>
1523	<td>Extract A.00h</td>
1524	<td>Bioplate A [C1]</td>
1525	</tr>
1526	<tr>
1527	<td>Labeled extract A.24h</td>
1528	<td>cy3</td>
1529	<td>Labeling A</td>
1530	<td>Extract A.24h</td>
1531	<td>Bioplate A [C2]</td>
1532	</tr>
1533	<tr>
1534	<td>Labeled extract A.ref</td>
1535	<td>cy5</td>
1536	<td>Labeling A</td>
1537	<td>Extract A.ref</td>
1538	<td>Bioplate A [C3]</td>
1539	</tr>
1540	<tr class="shaded">
1541	<td>Labeled extract A.00h (dye-swap)</td>
1542	<td>cy5</td>
1543	<td>Labeling A</td>
1544	<td>Extract A.00h</td>
1545	<td>Bioplate A [D1]</td>
1546	</tr>
1547	<tr class="shaded">
1548	<td>Labeled extract A.24h (dye-swap)</td>
1549	<td>cy5</td>
1550	<td>Labeling A</td>
1551	<td>Extract A.24h</td>
1552	<td>Bioplate A [D2]</td>
1553	</tr>
1554	<tr class="shaded">
1555	<td>Labeled extract A.ref (dye-swap)</td>
1556	<td>cy3</td>
1557	<td>Labeling A</td>
1558	<td>Extract A.ref</td>
1559	<td>Bioplate A [D3]</td>
1560	</tr>
1561	<tr>
1562	<td>Library A.00h</td>
1563	<td>-</td>
1564	<td>Library preparation A</td>
1565	<td>Extract A.00h</td>
1566	<td>Bioplate A [E1]</td>
1567	</tr>
1568	<tr>
1569	<td>Library A.24h</td>
1570	<td>-</td>
1571	<td>Library preparation A</td>
1572	<td>Extract A.24h</td>
1573	<td>Bioplate A [E2]</td>
1574	</tr>
1575	<tr>
1576	<td>Library A.ref</td>
1577	<td>-</td>
1578	<td>Library preparation A</td>
1579	<td>Extract A.ref</td>
1580	<td>Bioplate A [E3]</td>
1581	</tr>
1582	</table>
1583	<p>
1584	</li>
1585
1586	<li>
1587	Create physical bioassays (hybridizations and flow cells):
1588	<table class="listing" cellspacing="0" cellpadding="2" border="0">
1589	<tr>
1590	<th>Name</th>
1591	<th>Protocol</th>
1592	<th>Hardware</th>
1593	<th>Array slide</th>
1594	<th>Extracts (position)</th>
1595	</tr>
1596	<tr>
1597	<td>Hybridization A.00h</td>
1598	<td>Hybridization A</td>
1599	<td>Hybridization station A</td>
1600	<td>Array slide A.1</td>
1601	<td>Labeled extract A.00h,<br>Labeled extract A.ref</td>
1602	</tr>
1603	<tr>
1604	<td>Hybridization A.24h</td>
1605	<td>Hybridization A</td>
1606	<td>Hybridization station A</td>
1607	<td>Array slide A.2</td>
1608	<td>Labeled extract A.24h,<br>Labeled extract A.ref</td>
1609	</tr>
1610	<tr class="shaded">
1611	<td>Hybridization A.00h (dye-swap)</td>
1612	<td>Hybridization A</td>
1613	<td>Hybridization station A</td>
1614	<td>Array slide A.3</td>
1615	<td>Labeled extract A.00h (dye-swap),<br>Labeled extract A.ref (dye-swap)</td>
1616	</tr>
1617	<tr class="shaded">
1618	<td>Hybridization A.24h (dye-swap)</td>
1619	<td>Hybridization A</td>
1620	<td>Hybridization station A</td>
1621	<td>Array slide A.4</td>
1622	<td>Labeled extract A.24h (dye-swap),<br>Labeled extract A.ref (dye-swap)</td>
1623	</tr>
1624	<tr>
1625	<td>Affymetrix hyb A.1</td>
1626	<td>Hybridization A</td>
1627	<td>Hybridization station A</td>
1628	<td>Affymetrix slide A.1</td>
1629	<td>Labeled extract A.00h</td>
1630	</tr>
1631	<tr>
1632	<td>Affymetrix hyb A.2</td>
1633	<td>Hybridization A</td>
1634	<td>Hybridization station A</td>
1635	<td>Affymetrix slide A.2</td>
1636	<td>Labeled extract A.24h</td>
1637	</tr>
1638	<tr>
1639	<td>Affymetrix hyb A.3</td>
1640	<td>Hybridization A</td>
1641	<td>Hybridization station A</td>
1642	<td>Affymetrix slide A.3</td>
1643	<td>Labeled extract A.ref</td>
1644	</tr>
1645	<tr class="shaded">
1646	<td>Flow cell A</td>
1647	<td>cBot Settings A</td>
1648	<td>cBot A</td>
1649	<td>-</td>
1650	<td>Library A.00h (1),<br>Library A.24h (2)<br>Library A.ref (3)</td>
1651	</tr>
1652	</table>
1653	<p>
1654	</li>
1655
1656	<li>
1657	Create derived bioassays (scans, assemblys, etc.):
1658	<table class="listing" cellspacing="0" cellpadding="2" border="0">
1659	<tr>
1660	<th>Name</th>
1661	<th>Parent bioasasay</th>
1662	<th>Parent extract</th>
1663	<th>Hardware/Software</th>
1664	<th>Protocol</th>
1665	<th>PMT gain</th>
1666	</tr>
1667	<tr>
1668	<td>Scan A.00h</td>
1669	<td>Hybridization A.00h</td>
1670	<td>Labeled extract A.00h</td>
1671	<td>HW: Scanner A</td>
1672	<td>Scanning A</td>
1673	<td>400 V</td>
1674	</tr>
1675	<tr>
1676	<td>Scan A.24h</td>
1677	<td>Hybridization A.24h</td>
1678	<td>Labeled extract A.24h</td>
1679	<td>HW: Scanner A</td>
1680	<td>Scanning A</td>
1681	<td>500 V</td>
1682	</tr>
1683	<tr class="shaded">
1684	<td>Scan A.00h (dye-swap)</td>
1685	<td>Hybridization A.00h (dye-swap)</td>
1686	<td>Labeled extract A.00h (dye-swap)</td>
1687	<td>HW: Scanner A</td>
1688	<td>Scanning A</td>
1689	<td>600 V</td>
1690	</tr>
1691	<tr class="shaded">
1692	<td>Scan A.24h (dye-swap)</td>
1693	<td>Hybridization A.24h (dye-swap)</td>
1694	<td>Labeled extract A.24h (dye-swap)</td>
1695	<td>HW: Scanner A</td>
1696	<td>Scanning A</td>
1697	<td>700 V</td>
1698	</tr>
1699	<tr>
1700	<td>Affymetrix scan A.1</td>
1701	<td>Affymetrix hyb A.1</td>
1702	<td>Labeled extract A.00h</td>
1703	<td>HW: Scanner A</td>
1704	<td>Scanning A</td>
1705	<td>800 V</td>
1706	</tr>
1707	<tr>
1708	<td>Affymetrix scan A.2</td>
1709	<td>Affymetrix hyb A.2</td>
1710	<td>Labeled extract A.24h</td>
1711	<td>HW: Scanner A</td>
1712	<td>Scanning A</td>
1713	<td>900 V</td>
1714	</tr>
1715	<tr>
1716	<td>Affymetrix scan A.3</td>
1717	<td>Affymetrix hyb A.3</td>
1718	<td>Labeled extract A.ref</td>
1719	<td>HW: Scanner A</td>
1720	<td>Scanning A</td>
1721	<td>1000 V</td>
1722	</tr>
1723	<tr class="shaded">
1724	<td>Sequenced A</td>
1725	<td>Flow cell A</td>
1726	<td>-</td>
1727	<td>HW: HiSeq 2000 A</td>
1728	<td>HiSeq Settings A</td>
1729	<td>-</td>
1730	</tr>
1731	<tr class="shaded">
1732	<td>Assembly A.00h</td>
1733	<td>Sequenced A</td>
1734	<td>Library A.00h</td>
1735	<td>SW: TopHat</td>
1736	<td>TopHat Settings A</td>
1737	<td>-</td>
1738	</tr>
1739	<tr class="shaded">
1740	<td>Assembly A.24h</td>
1741	<td>Sequenced A</td>
1742	<td>Library A.24h</td>
1743	<td>SW: TopHat</td>
1744	<td>TopHat Settings A</td>
1745	<td>-</td>
1746	</tr>
1747	<tr class="shaded">
1748	<td>Assembly A.ref</td>
1749	<td>Sequenced A</td>
1750	<td>Library A.ref</td>
1751	<td>SW: TopHat</td>
1752	<td>TopHat Settings A</td>
1753	<td>-</td>
1754	</tr>
1755	</table>
1756	<p>
1757	</li>
1758
1759	<li>
1760	Add data files (TODO - we don't have any yet):
1761	<table class="listing" cellspacing="0" cellpadding="2" border="0">
1762	<tr>
1763	<th>Scan</th>
1764	<th>Data files</th>
1765	</tr>
1766	<tr>
1767	<td>Scan A.00h</td>
1768	<td>-</td>
1769	</tr>
1770	<tr>
1771	<td>Scan A.24h</td>
1772	<td>-</td>
1773	</tr>
1774	<tr class="shaded">
1775	<td>Scan A.00h (dye-swap)</td>
1776	<td>-</td>
1777	</tr>
1778	<tr class="shaded">
1779	<td>Scan A.24h (dye-swap)</td>
1780	<td>-</td>
1781	</tr>
1782	</table>
1783	<p>
1784	</li>
1785
1786	<li>
1787	Create raw bioassays:
1788	<table class="listing" cellspacing="0" cellpadding="2" border="0">
1789	<tr>
1790	<th>Name</th>
1791	<th>Platform/Raw data type</th>
1792	<th>Parent bioassay</th>
1793	<th>Parent extract</th>
1794	<th>Array design</th>
1795	<th>Protocol</th>
1796	<th>Software</th>
1797	<th>File(s)</th>
1798	</tr>
1799	<tr>
1800	<td>Raw bioassay A.00h</td>
1801	<td>Generic/GenePix</td>
1802	<td>Scan A.00h</td>
1803	<td>Labeled extract A.00h</td>
1804	<td>Array design A</td>
1805	<td>Feature extraction A</td>
1806	<td>Software A</td>
1807	<td><i>Raw data</i>: genepix.mouse.v4.37k.00h.gpr</td>
1808	</tr>
1809	<tr>
1810	<td>Raw bioassay A.24h</td>
1811	<td>Generic/GenePix</td>
1812	<td>Scan A.24h</td>
1813	<td>Labeled extract A.24h</td>
1814	<td>Array design A</td>
1815	<td>Feature extraction A</td>
1816	<td>Software A</td>
1817	<td><i>Raw data</i>: genepix.mouse.v4.37k.24h.gpr</td>
1818	</tr>
1819	<tr class="shaded">
1820	<td>Raw bioassay A.00h (dye-swap)</td>
1821	<td>Generic/GenePix</td>
1822	<td>Scan A.00h (dye-swap)</td>
1823	<td>Labeled extract A.00h (dye-swap)</td>
1824	<td>Array design A</td>
1825	<td>Feature extraction A</td>
1826	<td>Software A</td>
1827	<td><i>Raw data</i>: genepix.mouse.v4.37k.00h.dyeswap.gpr</td>
1828	</tr>
1829	<tr class="shaded">
1830	<td>Raw bioassay A.24h (dye-swap)</td>
1831	<td>Generic/GenePix</td>
1832	<td>Scan A.24h (dye-swap)</td>
1833	<td>Labeled extract A.24h (dye-swap)</td>
1834	<td>Array design A</td>
1835	<td>Feature extraction A</td>
1836	<td>Software A</td>
1837	<td><i>Raw data</i>: genepix.mouse.v4.37k.24h.dyeswap.gpr</td>
1838	</tr>
1839	<tr>
1840	<td>Affymetrix raw A.1</td>
1841	<td>Affymetrix</td>
1842	<td>Affymetrix scan A.1</td>
1843	<td>Labeled extract A.00h</td>
1844	<td>Affymetrix A</td>
1845	<td>Feature extraction A</td>
1846	<td>Software A</td>
1847	<td><i>CEL file</i>: jos1761.cel.bz2</td>
1848	</tr>
1849	<tr>
1850	<td>Affymetrix raw A.2</td>
1851	<td>Affymetrix</td>
1852	<td>Affymetrix scan A.2</td>
1853	<td>Labeled extract A.24h</td>
1854	<td>Affymetrix A</td>
1855	<td>Feature extraction A</td>
1856	<td>Software A</td>
1857	<td><i>CEL file</i>: jos1762.cel.bz2</td>
1858	</tr>
1859	<tr>
1860	<td>Affymetrix raw A.3</td>
1861	<td>Affymetrix</td>
1862	<td>Affymetrix scan A.3</td>
1863	<td>Labeled extract A.ref</td>
1864	<td>Affymetrix A</td>
1865	<td>Feature extraction A</td>
1866	<td>Software A</td>
1867	<td><i>CEL file</i>: jos1763.cel.bz2</td>
1868	</tr>
1869	<tr class="shaded">
1870	<td>SeqRaw A.00h</td>
1871	<td>Generic/GenePix</td>
1872	<td>Assembly A.00h</td>
1873	<td>Library A.00h</td>
1874	<td>Array design A</td>
1875	<td>Cufflinks Settings A</td>
1876	<td>Cufflinks</td>
1877	<td></td>
1878	</tr>
1879	<tr class="shaded">
1880	<td>SeqRaw A.24h</td>
1881	<td>Generic/GenePix</td>
1882	<td>Assembly A.24h</td>
1883	<td>Library A.24h</td>
1884	<td>Array design A</td>
1885	<td>Cufflinks Settings A</td>
1886	<td>Cufflinks</td>
1887	<td></td>
1888	</tr>
1889	<tr class="shaded">
1890	<td>SeqRaw A.ref</td>
1891	<td>Generic/GenePix</td>
1892	<td>Assembly A.ref</td>
1893	<td>Library A.ref</td>
1894	<td>Array design A</td>
1895	<td>Cufflinks Settings A</td>
1896	<td>Cufflinks</td>
1897	<td></td>
1898	</tr>
1899	</table>
1900	TODO - create other raw data type for sequence raw bioassays
1901	<p>
1902	</li>
1903	</ol>
1904
1905	<a name="step3"></a>
1906	<h3>Third step</h3>
1907	<ol>
1908	<li>
1909	Create experiments:
1910	<table class="listing" cellspacing="0" cellpadding="2" border="0">
1911	<tr>
1912	<th>Name</th>
1913	<th>Raw data type</th>
1914	<th>Raw bioassays</th>
1915	<th>Experimental factors</th>
1916	</tr>
1917	<tr>
1918	<td>Experiment A</td>
1919	<td>GenePix</td>
1920	<td>Raw bioassay A.00h,<br>Raw bioassay A.24h,<br>Raw bioassay A.00h (dye-swap),<br>
1921	Raw bioassay A.24h (dye-swap)</td>
1922	<td>Drug resistance, Time, Dye swap, PMT gain</td>
1923	</tr>
1924	<tr>
1925	<td>Affymetrix A</td>
1926	<td>Affymetrix</td>
1927	<td>Affymetrix raw A.1,<br>Affymetrix raw A.2,<br>Affymetrix raw A.3</td>
1928	<td>Drug resistance, Time, PMT gain</td>
1929	</tr>
1930	<tr>
1931	<td>Sequence A</td>
1932	<td>GenePix</td>
1933	<td>SeqRaw A.00h,<br>SeqRaw A.24h,<br>SeqRaw A.ref</td>
1934	<td>Drug resistance, Time</td>
1935	</tr>
1936	</table>
1937	<p>
1938	</li>
1939
1940	<li><a name="inheritannotations"></a>
1941	Inherit the annotations from the scans, samples and biosource for each raw bioassay.
1942	Use the <i>auto-inherit</i> function that exists on the experiment properties
1943	tab. Make sure that all experimental factors are selected by the check boxes,
1944	then click on the <i>Auto-inherit</i> link in the column header.
1945	Note! The <i>Dye swap</i>
1946	annotation will not get values until the next step, and the <i>Affymetrix raw A.3</i>
1947	data set is missing biomaterial parents with annotations.
1948	<p>
1949
1950	</li>
1951
1952	<li>
1953	Import GenePix raw data. There are two possible ways to do this:
1954	<ol>
1955	<li>Manually import to each raw bioassay.
1956	<li>Batch import to multiple raw bioassays.
1957	</ol>
1958	<p>
1959	<b>Manual import:</b> Go to the properties tab for each raw bioassay.
1960	Click on the <i>Import</i> button and use the auto-detect feature to
1961	import the raw data. Use the default configuration values except for
1962	those listed in the table below.
1963	<p>
1964
1965	<b>Batch import:</b> The batch import is started from the
1966	properties tab of the <i>experiment</i>. Click on "Import" and
1967	use the auto-detect feature with one of the used files. Use the default
1968	configuration values except for those listed in the table below.
1969	The batch import should import two raw data sets in one go (since it can
1970	only work with a single file format at a time and the dye-swap files uses
1971	a different file format). Repeat the batch import a second time to import
1972	the remaining two raw data sets.
1973	<p>
1974
1975	<table class="listing" cellspacing="0" cellpadding="2" border="0">
1976	<tr>
1977	<th>Parameter</th>
1978	<th>Value</th>
1979	<th>Mode</th>
1980	</tr>
1981	<tr>
1982	<td>Feature mismatch</td>
1983	<td>smart</td>
1984	<td>both</td>
1985	</tr>
1986	<tr>
1987	<td>Invalid numeric value</td>
1988	<td>null</td>
1989	<td>both</td>
1990	</tr>
1991	<tr>
1992	<td>Log file</td>
1993	<td>~/import.log</td>
1994	<td>batch import</td>
1995	</tr>
1996	</table>
1997	<p>
1998
1999	In both cases, the import should produce the same results
2000	as in the table below. When using the batch import mode, the
2001	detailed information for each raw bioassay is only found in
2002	the log file.
2003	<table class="listing" cellspacing="0" cellpadding="2" border="0">
2004	<tr>
2005	<th>Raw bioassay</th>
2006	<th>Raw data file</th>
2007	<th>Spots inserted/with null reporter/skipped)</th>
2008	<th>Annotations created</th>
2009	</tr>
2010	<tr>
2011	<td>Raw bioassay A.00h</td>
2012	<td>genepix.mouse.v4.37k.00h.gpr</td>
2013	<td>36,864/632/768</td>
2014	<td><i>Dye swap</i>: false</td>
2015	</tr>
2016	<tr>
2017	<td>Raw bioassay A.24h</td>
2018	<td>genepix.mouse.v4.37k.24h.gpr</td>
2019	<td>36,864/632/768</td>
2020	<td><i>Dye swap</i>: false</td>
2021	</tr>
2022	<tr class="shaded">
2023	<td>Raw bioassay A.00h (dye-swap)</td>
2024	<td>genepix.mouse.v4.37k.00h.dyeswap.gpr</td>
2025	<td>36,864/632/768</td>
2026	<td><i>Dye swap</i>: true</td>
2027	</tr>
2028	<tr class="shaded">
2029	<td>Raw bioassay A.24h (dye-swap)</td>
2030	<td>genepix.mouse.v4.37k.24h.dyeswap.gpr</td>
2031	<td>36,864/632/768</td>
2032	<td><i>Dye swap</i>: true</td>
2033	</tr>
2034	</table>
2035	<p>
2036
2037	</li>
2038
2039	<li>
2040	Check the experiment overview page. It should display one warnings for the
2041	Genepix experiment. The warning is related to a missing biosurce
2042	on the reference sample.
2043	<p>
2044	The Affymetrix experiment gives some more warnings. Most of them are
2045	related to not using the project default items, missing protocols
2046	and missing hardware. There should also be an error about missing
2047	experimental factor values for the <code>Affymetrix.3</code>
2048	raw bioassay. It is expected since this comes from the reference sample
2049	which doesn't have values for those annotations.
2050	<p>
2051
2052	Change validation options to reduce the number of warnings:
2053	<table class="listing" cellspacing="0" cellpadding="2" border="0">
2054	<tr>
2055	<th>Validation option</th>
2056	<th>Setting</th>
2057	</tr>
2058	<tr>
2059	<td>Project defaults</td>
2060	<td>Set all to <code>Ignore</code></td>
2061	</tr>
2062	<tr>
2063	<td>Missing items</td>
2064	<td>Set all to <code>Ignore</code></td>
2065	</tr>
2066	<tr>
2067	<td>Annotations - Missing factor value</td>
2068	<td><code>Warning</code></td>
2069	</tr>
2070	<tr>
2071	<td>Other - Raw spots <> features</td>
2072	<td><code>Ignore</code></td>
2073	</tr>
2074	</table>
2075
2076	After the changes there should now only be two warnings about the
2077	missing factor values.
2078
2079	<p>
2080	</li>
2081
2082	</ol>
2083	</li>
2084	</ol>
2085
2086	<a name="analysis"></a>
2087	<h2>6. Analysis tests</h2>
2088	<p>
2089	Now it is time to analyse the data. The analysis test should be done
2090	by both a regular user and a guest.
2091	</p>
2092
2093	<ol>
2094	<li>
2095	Activate the <code>Project A</code> project<p>
2096	</li>
2097
2098	<li>
2099	Go to the <code>Experiment A</code> experiment and select
2100	the <code>Bioassay sets</code> tab.
2101	<p>
2102	</li>
2103
2104	<li>
2105	Create a new root bioassay set:
2106	<table class="listing" cellspacing="0" cellpadding="2" border="0">
2107	<tr>
2108	<th>Bioassay set name</th>
2109	<th>Raw bioassays</th>
2110	<th>Formula</th>
2111	</tr>
2112	<tr>
2113	<td>Root bioassay set</td>
2114	<td>all</td>
2115	<td>Mean FG - Mean BG</td>
2116	</tr>
2117	</table>
2118	Wait for the plug-in to finish.
2119	<p>
2120	</li>
2121
2122	<li>
2123	Select the created bioassay set and create a filtered bioassayset:
2124	<table class="listing" cellspacing="0" cellpadding="2" border="0">
2125	<tr>
2126	<th>Child name</th>
2127	<th>Filter preset</th>
2128	<th>Expression</th>
2129	</tr>
2130	<tr>
2131	<td>Filtered bioassay set</td>
2132	<td>-</td>
2133	<td>ch(1) > 0 && ch(2) > 0 && rep('id') != null</td>
2134	</tr>
2135	</table>
2136	Wait for the plug-in to finish. It should report that 136,498 spots remain and
2137	that 10,958 spots has been removed.
2138	<p>
2139	</li>
2140
2141	<li>
2142	Select the filtered bioassay set and run a normalization plug-in:
2143	<table class="listing" cellspacing="0" cellpadding="2" border="0">
2144	<tr>
2145	<th>Plugin</th>
2146	<th>Parameters</th>
2147	</tr>
2148	<tr>
2149	<td>Normalization: Lowess</td>
2150	<td>Accept the default parameters.</td>
2151	</tr>
2152	</table>
2153	Wait for the plug in to finish. It should report that 136,498 spots has been
2154	normalized and 0 spots has been removed.
2155	<p>
2156	</li>
2157
2158	<li>
2159	Select the normalized bioassay set and check the MA plots and
2160	the correction factor plots. Here are four examples:
2161	<table class="listing" cellspacing="0" cellpadding="2" border="0">
2162	<tr>
2163	<th>MA plots</th>
2164	<th>Correction factor plots</th>
2165	</tr>
2166	<tr>
2167	<td><img src="overview.png"><br><img src="overview.dyeswap.png"></td>
2168	<td><img src="correction.png"><br><img src="correction.dyeswap.png"></td>
2169	</tr>
2170	</table>
2171	<p>
2172	</li>
2173
2174	<li>
2175	Try the plot tool with the following plots. Use the <code>Save</code> function
2176	to save one them as a file in the BASE file system, and the <code>Download</code>
2177	function to download a plot to your computer.
2178	<table class="listing" cellspacing="0" cellpadding="2" border="0">
2179	<tr>
2180	<th>Plot type</th>
2181	<th>Y-axis preset</th>
2182	<th>X-axis preset</th>
2183	<th>Other options</th>
2184	</tr>
2185	<tr>
2186	<td>Scatter plot</td>
2187	<td>M, log2(ch1 / ch2)</td>
2188	<td>A, log10(ch1 * ch2) / 2</td>
2189	<td>-</td>
2190	</tr>
2191	<tr>
2192	<td>Histogram plot</td>
2193	<td>Count</td>
2194	<td>Ratio, ch1 / ch2</td>
2195	<td>
2196	<table border="0" cellspacing="0" cellpadding="2">
2197	<tr>
2198	<td><i>Log scale</i></td>
2199	<td>checked</td>
2200	</tr>
2201	<tr>
2202	<td><i>Bin size</i></td>
2203	<td>0.1</td>
2204	</tr>
2205	<tr>
2206	<td><i>Annotation</i></td>
2207	<td>Time</td>
2208	</tr>
2209	</table>
2210	</td>
2211	</tr>
2212	</table>
2213	<p>
2214	Here are two examples:
2215	<table class="listing" cellspacing="0" cellpadding="2" border="0">
2216	<tr>
2217	<th>Scatter plot</th>
2218	</tr>
2219	<tr>
2220	<td><img src="scatter.png"></td>
2221	</tr>
2222	</table>
2223	<p>
2224	<table class="listing" cellspacing="0" cellpadding="2" border="0">
2225	<tr>
2226	<th>Histogram plot</th>
2227	</tr>
2228	<tr>
2229	<td><img src="histogram.png"></td>
2230	</tr>
2231	</table>
2232	<p>
2233	</li>
2234
2235	</ol>
2236
2237
2238	</body>
2239	</html>

Note: See TracBrowser for help on using the repository browser.

Context Navigation

source: trunk/doc/test/roles/index.html @ 5699

Download in other formats: