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Last change on this file since 5700 was 5700, checked in by Nicklas Nordborg, 12 years ago

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

Fixed batch importer tests. Beware that the tab-separated text files are a bit different than those used by BASE 2.17 and before.

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3	$Id: index.html 5700 2011-08-17 10:38:19Z nicklas $
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5	Copyright (C) 2006 Jari Häkkinen, Nicklas Nordborg, Martin Svensson
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8	Available at http://base.thep.lu.se/
9
10	BASE is free software; you can redistribute it and/or
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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: 2011-08-17 10:38:19 +0000 (Wed, 17 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	</ul>
175	</li>
176
177	</ol>
178
179	<a name="root"></a>
180	<h2>2. Root user tests</h2>
181	<p>
182	The root user creates an administrator which is a server-wide admin.
183	</p>
184
185	<ol>
186	<li>
187	Create a new user and set the following
188	properties. All other properties may remain unchanged.
189
190	<table class="listing" cellspacing="0" cellpadding="2" border="0">
191	<tr>
192	<th>Name</th>
193	<th>Login/Password</th>
194	<th>Quota</th>
195	<th>Quota group</th>
196	<th>Membership</th>
197	</tr>
198	<tr>
199	<td>Admin</td>
200	<td>admin/admin</td>
201	<td>Unlimited</td>
202	<td>-</td>
203	<td>Roles: Administrator</td>
204	</tr>
205	</table>
206	</li>
207	</ol>
208
209	<a name="admin"></a>
210	<h2>3. Administrator tests</h2>
211	<p>
212	The administrator creates users for a project and gives them permissions
213	that are suitable for their role in the project. The administrator also
214	sets up quota and group membership.
215	</p>
216
217	<ol>
218	<li>
219	Create a new group and set the following properties:
220
221	<table class="listing" cellspacing="0" cellpadding="2" border="0">
222	<tr>
223	<th>Name</th>
224	<th>Quota</th>
225	</tr>
226	<tr>
227	<td>Group A</td>
228	<td>1GB</td>
229	</tr>
230	</table>
231	<p>
232	</li>
233
234	<li>
235	Create the following users:
236
237	<table class="listing" cellspacing="0" cellpadding="2" border="0">
238	<tr>
239	<th>Name</th>
240	<th>Login/Password</th>
241	<th>Quota</th>
242	<th>Quota group</th>
243	<th>Membership</th>
244	<th>Other</th>
245	</tr>
246	<tr>
247	<td>Power user</td>
248	<td>power/power</td>
249	<td>1GB</td>
250	<td>Group A</td>
251	<td>Roles: Power user</td>
252	<td>-</td>
253	</tr>
254	<tr>
255	<td>User</td>
256	<td>user/user</td>
257	<td>1GB</td>
258	<td>Group A</td>
259	<td>Roles: User</td>
260	<td>-</td>
261	</tr>
262	<tr>
263	<td>Guest</td>
264	<td>guest/guest</td>
265	<td>10MB</td>
266	<td>Group A</td>
267	<td>Roles: Guest</td>
268	<td><i>Multi-user account</i> checked</td>
269	</tr>
270	</table>
271	<p>
272	</li>
273
274	<li>Give USE permission for the listed users to the following plugins:
275
276	<table class="listing" cellspacing="0" cellpadding="2" border="0">
277	<tr>
278	<th>User</th>
279	<th>Plugins</th>
280	</tr>
281	<tr>
282	<td>Power user</td>
283	<td>
284	<ul>
285	<li>Plate importer</li>
286	<li>Reporter map importer</li>
287	<li>Print map importer</li>
288	<li>Array design importer</li>
289	<li>Array batch importer</li>
290	<li>Array slide importer</li>
291	</ul>
292	</td>
293	</tr>
294	</table>
295	<p>
296	</li>
297
298	<li>
299	Create file formats (<i>i.e.</i>, plug-in configurations) for importing
300	reporters. The formats marked as
301	optional are not used in the test procedure, but may be useful to weed
302	out import problems, since they allow importing all info from the raw
303	data files. You may either enter the regular expressions as specified or
304	use the "Test with file" feature.
305
306	<table class="listing" cellspacing="0" cellpadding="2" border="0">
307	<tr>
308	<th>Name</th>
309	<th>Plugin</th>
310	<th>Configuration values</th>
311	</tr>
312	<tr class="oddrow">
313	<td>Reporters for project A</td>
314	<td>Reporter importer</td>
315	<td>
316	<b>Test with file:</b> <code>plates_and_reporters.mouse.v4.37k.txt</code>
317	<table border="0" cellspacing="0" cellpadding="2">
318	<tr>
319	<td><i>Data header</i></td>
320	<td>384_number\t384_column\t384_row\t384_position\toligo_id.*</td>
321	</tr>
322	<tr>
323	<td><i>Data splitter</i></td>
324	<td>\t</td>
325	</tr>
326	<tr>
327	<td><i>Min data columns</i></td>
328	<td>5</td>
329	</tr>
330	<tr>
331	<td><i>Name</i></td>
332	<td>\oligo_id\</td>
333	</tr>
334	<tr>
335	<td><i>External ID</i></td>
336	<td>\oligo_id\</td>
337	</tr>
338	<tr>
339	<td><i>Description</i></td>
340	<td>\description_Ensembl*\</td>
341	</tr>
342	<tr>
343	<td><i>Gene symbol</i></td>
344	<td>\gene_symbol_Ensembl*\</td>
345	</tr>
346	<tr>
347	<td><i>Sequence</i></td>
348	<td>\oligo_sequence\</td>
349	</tr>
350	</table>
351
352	</td>
353	</tr>
354
355	<tr class="evenrow">
356	<td>GenePix reporter importer<br>(optional)</td>
357	<td>Reporter importer</td>
358	<td>
359
360	<b>Test with file:</b> <code>genepix.mouse.v4.37k.00h.gpr</code>
361	<table border="0" cellspacing="0" cellpadding="2">
362	<tr>
363	<td><i>Data header</i></td>
364	<td>"Block"\t"Column"\t"Row"\t"Name"\t"ID"\t.*</td>
365	</tr>
366	<tr>
367	<td><i>Data splitter</i></td>
368	<td>\t</td>
369	</tr>
370	<tr>
371	<td><i>Min data columns</i></td>
372	<td>48</td>
373	</tr>
374	<tr>
375	<td><i>Max data columns</i></td>
376	<td>48</td>
377	</tr>
378	<tr>
379	<td><i>Name</i></td>
380	<td>\Name\</td>
381	</tr>
382	<tr>
383	<td><i>External ID</i></td>
384	<td>\ID\</td>
385	</tr>
386	</table>
387
388	</td>
389	</tr>
390	<tr class="oddrow">
391	<td>Reporters from Affymetrix annotations file</td>
392	<td>Reporter importer</td>
393	<td>
394	<b>Test with file:</b> <code>MG_U74Av2_annot.csv.bz2</code>
395	<table border="0" cellspacing="0" cellpadding="2">
396	<tr>
397	<td><i>Data header</i></td>
398	<td>"Probe Set ID","GeneChip Array".*</td>
399	</tr>
400	<tr>
401	<td><i>Data splitter</i></td>
402	<td>(?!"),(?=")</td>
403	</tr>
404	<tr>
405	<td><i>Name</i></td>
406	<td>\Probe Set ID\</td>
407	</tr>
408	<tr>
409	<td><i>External ID</i></td>
410	<td>\Probe Set ID\</td>
411	</tr>
412	<tr>
413	<td><i>Description</i></td>
414	<td>\Target Description\</td>
415	</tr>
416	<tr>
417	<td><i>Gene symbol</i></td>
418	<td>\Gene Symbol\</td>
419	</tr>
420	</table>
421
422	</td>
423	</tr>
424	</table>
425	<p>
426	</li>
427
428	<li>
429	Import reporters:
430	<ol>
431	<li>Go to the <code>View -> Reporters</code> page.</li>
432	<li>Click on the <code>Import</code> button.</li>
433	<li>Choose <code>auto-detect</code> and then upload
434	the file <code>plates_and_reporters.mouse.v4.37k.txt</code>.</li>
435	<li>The <code>Reporters for project A</code> format should be
436	found.</li>
437	<li>Select the <code>skip</code> option for the "Missing a required" value
438	since the file contains rows with empty reporter ID:s.
439	<li>Continue and wait for the import to finish. It should create 35,912 new reporters.</li>
440	<li>
441	Repeat the procedure with the <code>MG_U74Av2_annot.csv</code> file. This time
442	also select <code>crop</code> for the "String too long" setting since
443	the file contains data that is too large for the datbase.
444	12,488 new reporters should be created.
445	</ol>
446	<p>
447
448	</li>
449
450
451	</ol>
452
453
454	<a name="power"></a>
455	<h2>4. Power user tests</h2>
456	<p>
457	The power user is the typical owner/administrator of a project. The power user sets
458	up common resources used in the project, such as hardware, software, protocols,
459	file formats and annotation types. In this case the power user is also responsible for
460	managing the LIMS.
461	</p>
462
463	<ol>
464	<li>
465	Create a project:
466
467	<table class="listing" cellspacing="0" cellpadding="2" border="0">
468	<tr>
469	<th>Name</th>
470	<th>Members</th>
471	</tr>
472	<tr>
473	<td>Project A</td>
474	<td>Groups: Group A (Use permission)</td>
475	</tr>
476	</table>
477	<p>
478	</li>
479
480	<li>Activate the project.<p></li>
481
482	<li>
483	Create annotation types [A] and protocol parameters [P]:
484	<table class="listing" cellspacing="0" cellpadding="2" border="0">
485	<tr>
486	<th>Name</th>
487	<th>Type</th>
488	<th>Unit</th>
489	<th>Interface</th>
490	<th>Values</th>
491	<th>Item types</th>
492	</tr>
493	<tr>
494	<td>Drug resistance [A]</td>
495	<td>String</td>
496	<td>-</td>
497	<td>radiobuttons</td>
498	<td>high, medium, low</td>
499	<td>Biosource</td>
500	</tr>
501	<tr>
502	<td>Time [A]</td>
503	<td>Integer</td>
504	<td>Hour</td>
505	<td>text box</td>
506	<td>-</td>
507	<td>Sample</td>
508	</tr>
509	<tr>
510	<td>Dye swap [A]</td>
511	<td>Boolean</td>
512	<td>-</td>
513	<td>-</td>
514	<td>-</td>
515	<td>Raw bioassay</td>
516	</tr>
517	<tr>
518	<td>PMT gain [P]</td>
519	<td>Float</td>
520	<td>Volt (Electric potential)</td>
521	<td>-</td>
522	<td>-</td>
523	<td>Scan</td>
524	</tr>
525	</table>
526	<p>
527	</li>
528
529	<li>
530	Create protocols:
531	<table class="listing" cellspacing="0" cellpadding="2" border="0">
532	<tr>
533	<th>Name</th>
534	<th>Type</th>
535	<th>Comment</th>
536	</tr>
537	<tr>
538	<td>Sampling A</td>
539	<td>Sampling</td>
540	</tr>
541	<tr>
542	<td>Extraction A</td>
543	<td>Extraction</td>
544	</tr>
545	<tr>
546	<td>Labeling A</td>
547	<td>Labeling</td>
548	</tr>
549	<tr>
550	<td>Library preparation A</td>
551	<td>Library preparation</td>
552	</tr>
553	<tr>
554	<td>Hybridization A</td>
555	<td>Hybridization</td>
556	</tr>
557	<tr>
558	<td>cBot Settings A</td>
559	<td>Cluster generation</td>
560	</tr>
561	<tr>
562	<td>Scanning A</td>
563	<td>Scanning</td>
564	<td>Select 'PMT gain' as a protocol parameter.</td>
565	</tr>
566	<tr>
567	<td>HiSeq Settings A</td>
568	<td>Sequencing</td>
569	</tr>
570	<tr>
571	<td>TopHat Settings A</td>
572	<td>Alignment</td>
573	</tr>
574	<tr>
575	<td>Feature extraction A</td>
576	<td>Feature extraction</td>
577	</tr>
578	<tr>
579	<td>Cufflinks Settings A</td>
580	<td>Feature extraction</td>
581	</tr>
582	<tr>
583	<td>Printing A</td>
584	<td>Printing</td>
585	</tr>
586	</table>
587	<p>
588	</li>
589
590	<li>
591	Create hardware:
592	<table class="listing" cellspacing="0" cellpadding="2" border="0">
593	<tr>
594	<th>Name</th>
595	<th>Type</th>
596	</tr>
597	<tr>
598	<td>Hybridization station A</td>
599	<td>Hybridization station</td>
600	</tr>
601	<tr>
602	<td>cBot A</td>
603	<td>Cluster generator</td>
604	</tr>
605	<tr>
606	<td>HiSeq 2000 A</td>
607	<td>Sequencer</td>
608	</tr>
609	<tr>
610	<td>Scanner A</td>
611	<td>Scanner</td>
612	</tr>
613	<tr>
614	<td>Print robot A</td>
615	<td>Print robot</td>
616	</tr>
617	</table>
618	<p>
619	</li>
620
621	<li>
622	Create software:
623	<table class="listing" cellspacing="0" cellpadding="2" border="0">
624	<tr>
625	<th>Name</th>
626	<th>Type</th>
627	</tr>
628	<tr>
629	<td>Software A</td>
630	<td>Feature extraction</td>
631	</tr>
632	</table>
633	<p>
634	</li>
635
636	<li>
637	Create bioplate type:
638	<table class="listing" cellspacing="0" cellpadding="2" border="0">
639	<tr>
640	<th>Name</th>
641	<th>Biomaterial type</th>
642	<th>Well lock mode</th>
643	</tr>
644	<tr>
645	<td>Bioplate type A</td>
646	<td>Any</td>
647	<td>Unlocked</td>
648	</tr>
649	</table>
650	<p>
651	</li>
652
653	<li>
654	Create file formats (<i>i.e.</i>, plug-in configurations). The formats marked as
655	optional are not used in the test procedure, but may be useful to weed
656	out import problems, since they allow importing all info from the raw
657	data files. You may either enter the regular expressions as specified or
658	use the "Test with file" feature.
659
660	<table class="listing" cellspacing="0" cellpadding="2" border="0">
661	<tr>
662	<th>Name</th>
663	<th>Plugin</th>
664	<th>Configuration values</th>
665	</tr>
666
667	<tr class="oddrow">
668	<td>Plates for project A</td>
669	<td>Plate importer</td>
670	<td>
671
672	<b>Test with file:</b> <code>plates_and_reporters.mouse.v4.37k.txt</code>
673	<table border="0" cellspacing="0" cellpadding="2">
674	<tr>
675	<td><i>Data header</i></td>
676	<td>384_number\t384_column\t384_row\t384_position\toligo_id.*</td>
677	</tr>
678	<tr>
679	<td><i>Data splitter</i></td>
680	<td>\t</td>
681	</tr>
682	<tr>
683	<td><i>Min data columns</i></td>
684	<td>5</td>
685	</tr>
686	<tr>
687	<td><i>Plate number/name</i></td>
688	<td>\384_number\</td>
689	</tr>
690	<tr>
691	<td><i>Row</i></td>
692	<td>\384_row\</td>
693	</tr>
694	<tr>
695	<td><i>Column</i></td>
696	<td>\384_column\</td>
697	</tr>
698	<tr>
699	<td><i>Reporter ID</i></td>
700	<td>\oligo_id\</td>
701	</tr>
702	</table>
703
704	</td>
705	</tr>
706
707	<tr class="evenrow">
708	<td>GenePix feature importer<br>(optional)</td>
709	<td>Reporter map importer</td>
710	<td>
711
712	<b>Test with file:</b> <code>genepix.mouse.v4.37k.00h.gpr</code>
713	<table border="0" cellspacing="0" cellpadding="2">
714	<tr>
715	<td><i>Data header</i></td>
716	<td>"Block"\t"Column"\t"Row"\t"Name"\t"ID"\t.*</td>
717	</tr>
718	<tr>
719	<td><i>Data splitter</i></td>
720	<td>\t</td>
721	</tr>
722	<tr>
723	<td><i>Min data columns</i></td>
724	<td>48</td>
725	</tr>
726	<tr>
727	<td><i>Max data columns</i></td>
728	<td>48</td>
729	</tr>
730	<tr>
731	<td><i>Reporter ID</i></td>
732	<td>\ID\</td>
733	</tr>
734	<tr>
735	<td><i>Block</i></td>
736	<td>\Block\</td>
737	</tr>
738	<tr>
739	<td><i>Column</i></td>
740	<td>\Column\</td>
741	</tr>
742	<tr>
743	<td><i>Row</i></td>
744	<td>\Row\</td>
745	</tr>
746	</table>
747
748	</td>
749	</tr>
750
751	<tr class="oddrow">
752	<td>Raw data for project A</td>
753	<td>Raw data importer</td>
754	<td>
755
756	<b>Test with file:</b> <code>genepix.mouse.v4.37k.00h.gpr</code>
757	<table border="0" cellspacing="0" cellpadding="2">
758	<tr>
759	<td><i>Raw data type</i></td>
760	<td>Genepix</td>
761	</tr>
762	<tr>
763	<td><i>Header</i></td>
764	<td>"(.+)=(.*)"</td>
765	</tr>
766	<tr>
767	<td><i>Data header</i></td>
768	<td>"Block"\t"Column"\t"Row"\t"Name"\t"ID"\t."Ratio of Medians $532\/635$".</td>
769	</tr>
770	<tr>
771	<td><i>Data splitter</i></td>
772	<td>\t</td>
773	</tr>
774	<tr>
775	<td><i>Min data columns</i></td>
776	<td>48</td>
777	</tr>
778	<tr>
779	<td><i>Max data columns</i></td>
780	<td>48</td>
781	</tr>
782
783	<tr>
784	<td><i>Block</i></td>
785	<td>\Block\</td>
786	</tr>
787	<tr>
788	<td><i>Column</i></td>
789	<td>\Column\</td>
790	</tr>
791	<tr>
792	<td><i>Row</i></td>
793	<td>\Row\</td>
794	</tr>
795	<tr>
796	<td><i>X</i></td>
797	<td>\X\</td>
798	</tr>
799	<tr>
800	<td><i>Y</i></td>
801	<td>\Y\</td>
802	</tr>
803	<tr>
804	<td><i>Reporter ID</i></td>
805	<td>\ID\</td>
806	</tr>
807	<tr>
808	<td><i>Spot diameter</i></td>
809	<td>\Dia.\</td>
810	</tr>
811	<tr>
812	<td><i>Channel 1 foreground median</i></td>
813	<td>\F635 Median\</td>
814	</tr>
815	<tr>
816	<td><i>Channel 1 foreground mean</i></td>
817	<td>\F635 Mean\</td>
818	</tr>
819	<tr>
820	<td><i>Channel 1 foreground standard deviation</i></td>
821	<td>\F635 SD\</td>
822	</tr>
823	<tr>
824	<td><i>Channel 1 background median</i></td>
825	<td>\B635 Median\</td>
826	</tr>
827	<tr>
828	<td><i>Channel 1 background mean</i></td>
829	<td>\B635 Mean\</td>
830	</tr>
831	<tr>
832	<td><i>Channel 1 background standard deviation</i></td>
833	<td>\B635 SD\</td>
834	</tr>
835	<tr>
836	<td><i>Percent pixels within 1 standard deviation</i></td>
837	<td>\% > B635+1SD\</td>
838	</tr>
839	<tr>
840	<td><i>Percent pixels within 2 standard deviations</i></td>
841	<td>\% > B635+2SD\</td>
842	</tr>
843	<tr>
844	<td><i>Percent saturated pixels</i></td>
845	<td>\F635 % Sat.\</td>
846	</tr>
847	<tr>
848	<td><i>Channel 2 foreground median</i></td>
849	<td>\F532 Median\</td>
850	</tr>
851	<tr>
852	<td><i>Channel 2 foreground mean</i></td>
853	<td>\F532 Mean\</td>
854	</tr>
855	<tr>
856	<td><i>Channel 2 foreground standard deviation</i></td>
857	<td>\F532 SD\</td>
858	</tr>
859	<tr>
860	<td><i>Channel 2 background median</i></td>
861	<td>\B532 Median\</td>
862	</tr>
863	<tr>
864	<td><i>Channel 2 background mean</i></td>
865	<td>\B532 Mean\</td>
866	</tr>
867	<tr>
868	<td><i>Channel 2 background standard deviation</i></td>
869	<td>\B532 SD\</td>
870	</tr>
871	<tr>
872	<td><i>Percent pixels within 1 standard deviation</i></td>
873	<td>\% > B532+1SD\</td>
874	</tr>
875	<tr>
876	<td><i>Percent pixels within 2 standard deviations</i></td>
877	<td>\% > B532+2SD\</td>
878	</tr>
879	<tr>
880	<td><i>Percent saturated pixels</i></td>
881	<td>\F532 % Sat.\</td>
882	</tr>
883	<tr>
884	<td><i>Foreground pixels</i></td>
885	<td>\F Pixels\</td>
886	</tr>
887	<tr>
888	<td><i>Background pixels</i></td>
889	<td>\B Pixels\</td>
890	</tr>
891	<tr>
892	<td><i>Flags</i></td>
893	<td>\Flags\</td>
894	</tr>
895	</table>
896
897	</td>
898	</tr>
899
900	<tr class="evenrow">
901	<td>Raw data for project A (dye-swap)</td>
902	<td>Raw data importer</td>
903	<td>
904
905	<b>Test with file:</b> <code>genepix.mouse.v4.37k.00h.dyeswap.gpr</code>
906	<table border="0" cellspacing="0" cellpadding="2">
907	<tr>
908	<td><i>Raw data type</i></td>
909	<td>Genepix</td>
910	</tr>
911	<tr>
912	<td><i>Header</i></td>
913	<td>"(.+)=(.*)"</td>
914	</tr>
915	<tr>
916	<td><i>Data header</i></td>
917	<td>"Block"\t"Column"\t"Row"\t"Name"\t"ID"\t."Ratio of Medians $635\/532$".</td>
918	</tr>
919	<tr>
920	<td><i>Data splitter</i></td>
921	<td>\t</td>
922	</tr>
923	<tr>
924	<td><i>Min data columns</i></td>
925	<td>48</td>
926	</tr>
927	<tr>
928	<td><i>Max data columns</i></td>
929	<td>48</td>
930	</tr>
931
932	<tr>
933	<td><i>Block</i></td>
934	<td>\Block\</td>
935	</tr>
936	<tr>
937	<td><i>Column</i></td>
938	<td>\Column\</td>
939	</tr>
940	<tr>
941	<td><i>Row</i></td>
942	<td>\Row\</td>
943	</tr>
944	<tr>
945	<td><i>X</i></td>
946	<td>\X\</td>
947	</tr>
948	<tr>
949	<td><i>Y</i></td>
950	<td>\Y\</td>
951	</tr>
952	<tr>
953	<td><i>Reporter ID</i></td>
954	<td>\ID\</td>
955	</tr>
956	<tr>
957	<td><i>Spot diameter</i></td>
958	<td>\Dia.\</td>
959	</tr>
960	<tr>
961	<td><i>Channel 1 foreground median</i></td>
962	<td>\F532 Median\</td>
963	</tr>
964	<tr>
965	<td><i>Channel 1 foreground mean</i></td>
966	<td>\F532 Mean\</td>
967	</tr>
968	<tr>
969	<td><i>Channel 1 foreground standard deviation</i></td>
970	<td>\F532 SD\</td>
971	</tr>
972	<tr>
973	<td><i>Channel 1 background median</i></td>
974	<td>\B532 Median\</td>
975	</tr>
976	<tr>
977	<td><i>Channel 1 background mean</i></td>
978	<td>\B532 Mean\</td>
979	</tr>
980	<tr>
981	<td><i>Channel 1 background standard deviation</i></td>
982	<td>\B532 SD\</td>
983	</tr>
984	<tr>
985	<td><i>Percent pixels within 1 standard deviation</i></td>
986	<td>\% > B532+1SD\</td>
987	</tr>
988	<tr>
989	<td><i>Percent pixels within 2 standard deviations</i></td>
990	<td>\% > B532+2SD\</td>
991	</tr>
992	<tr>
993	<td><i>Percent saturated pixels</i></td>
994	<td>\F532 % Sat.\</td>
995	</tr>
996	<tr>
997	<td><i>Channel 2 foreground median</i></td>
998	<td>\F635 Median\</td>
999	</tr>
1000	<tr>
1001	<td><i>Channel 2 foreground mean</i></td>
1002	<td>\F635 Mean\</td>
1003	</tr>
1004	<tr>
1005	<td><i>Channel 2 foreground standard deviation</i></td>
1006	<td>\F635 SD\</td>
1007	</tr>
1008	<tr>
1009	<td><i>Channel 2 background median</i></td>
1010	<td>\B635 Median\</td>
1011	</tr>
1012	<tr>
1013	<td><i>Channel 2 background mean</i></td>
1014	<td>\B635 Mean\</td>
1015	</tr>
1016	<tr>
1017	<td><i>Channel 2 background standard deviation</i></td>
1018	<td>\B635 SD\</td>
1019	</tr>
1020	<tr>
1021	<td><i>Percent pixels within 1 standard deviation</i></td>
1022	<td>\% > B635+1SD\</td>
1023	</tr>
1024	<tr>
1025	<td><i>Percent pixels within 2 standard deviations</i></td>
1026	<td>\% > B635+2SD\</td>
1027	</tr>
1028	<tr>
1029	<td><i>Percent saturated pixels</i></td>
1030	<td>\F635 % Sat.\</td>
1031	</tr>
1032	<tr>
1033	<td><i>Foreground pixels</i></td>
1034	<td>\F Pixels\</td>
1035	</tr>
1036	<tr>
1037	<td><i>Background pixels</i></td>
1038	<td>\B Pixels\</td>
1039	</tr>
1040	<tr>
1041	<td><i>Flags</i></td>
1042	<td>\Flags\</td>
1043	</tr>
1044	</table>
1045
1046	</td>
1047	</tr>
1048	</table>
1049	<p>
1050	</li>
1051
1052	<li>
1053	Annotate the file formats:
1054	<table class="listing" cellspacing="0" cellpadding="2" border="0">
1055	<tr>
1056	<th>File format</th>
1057	<th>Annotation</th>
1058	<th>Value</th>
1059	</tr>
1060	<tr>
1061	<td>Raw data for project A</td>
1062	<td>Dye swap</td>
1063	<td>false</td>
1064	</tr>
1065	<tr>
1066	<td>Raw data for project A (dye swap)</td>
1067	<td>Dye swap</td>
1068	<td>true</td>
1069	</tr>
1070	</table>
1071	This will make the raw data importer automatically annotate the
1072	raw bioassays with the specified annotations.
1073	<p>
1074	</li>
1075
1076	<li>
1077	Create plate type:
1078	<table class="listing" cellspacing="0" cellpadding="2" border="0">
1079	<tr>
1080	<th>Name</th>
1081	<th>Geometry</th>
1082	</tr>
1083	<tr>
1084	<td>Plate type A</td>
1085	<td>384-well (16 x 24)</td>
1086	</tr>
1087	</table>
1088	<p>
1089	</li>
1090
1091	<li>
1092	Import plates:
1093	<ol>
1094	<li>Go to the <code>Array LIMS -> Plates</code> page.</li>
1095	<li>Click on the <code>Import</code> button.</li>
1096	<li>Choose <code>auto-detect</code> and select
1097	the file <code>plates_and_reporters.mouse.v4.37k.txt</code>.</li>
1098	<li>The <code>Plates for project A</code> format should be
1099	found.</li>
1100	<li>Specify the following parameters:
1101
1102	<table border="0" cellspacing="0" cellpadding="2">
1103	<tr>
1104	<td><i>Plate type</i></td>
1105	<td>Plate type A</td>
1106	</tr>
1107	<tr>
1108	<td><i>Plate name prefix</i></td>
1109	<td>Plate A</td>
1110	</tr>
1111	<tr>
1112	<td><i>Plate name padding</i></td>
1113	<td>4</td>
1114	</tr>
1115	</table>
1116	</li>
1117	<li>Continue and wait for the import to finish. It should create 96 plates.</li>
1118	</ol>
1119	<p>
1120	</li>
1121
1122	<li>
1123	Create array designs and upload data files to them:
1124	<table class="listing" cellspacing="0" cellpadding="2" border="0">
1125	<tr>
1126	<th>Name</th>
1127	<th>Platform</th>
1128	<th>File(s)</th>
1129	</tr>
1130	<tr>
1131	<td>Array design A</td>
1132	<td>Generic</td>
1133	<td><i>Print map</i>: printmap.mouse.v4.37k.tam</td>
1134	</tr>
1135	<tr>
1136	<td>Affymetrix A</td>
1137	<td>Affymetrix</td>
1138	<td><i>CDF file</i>: MG_U74Av2.cdf.bz2</td>
1139	</tr>
1140	</table>
1141	<p>
1142	Or
1143	<p>
1144	Import array designs with the ArrayDesignImporter plug-in.
1145	<ol>
1146	<li>Make sure the data-files, mentioned in table above, are located in <code>/home/power/</code>, upload them if not</li>
1147	<li>Click on the <code>Import</code> button on the array design list page.</li>
1148	<li>Choose ArrayDesignImporter in the plug-in drop-down list.</li>
1149	<li><b>Test with file:</b> <code>arraydesign_out.txt</code> and set
1150	the parsing parameters with help of the <code>Auto generate</code> button on the <code>Column mapping</code>
1151	tab.</li>
1152	<li>Start the import-job by clicking on the <code>Finish</code> button on the third wizard-page.</li>
1153	</ol>
1154	<p>
1155	</li>
1156
1157	<li>
1158	Connect <code>Array design A</code> with plates. Select the imported plates (plate names starting
1159	with <code>Plate A</code>) and sort them in the correct order (as indicated by their names).
1160	<p>
1161	</li>
1162
1163	<li>
1164	Import features:
1165	<ol>
1166	<li>Click on the <code>Import</code> button when viewing properties for the array design.</li>
1167	<li>Choose <code>auto-detect</code> and upload the file
1168	<code>printmap.mouse.v4.37k.tam</code>.</li>
1169	<li>The <code>Print map importer</code> plug-in should be
1170	found.</li>
1171	<li>Continue and wait for the import to finish. It should create 36,864 features and 48 blocks.</li>
1172	</ol>
1173	<p>
1174	</li>
1175
1176	<li>
1177	Set project defaults. Go to the projects page and edit the
1178	<code>Project A</code> project. On the <code>Defaults</code>
1179	tab, set the following defaults:
1180
1181	<table class="listing" cellspacing="0" cellpadding="2" border="0">
1182	<tr>
1183	<th>Setting</th>
1184	<th>Value(s)</th>
1185	</tr>
1186	<tr>
1187	<td>Raw data type</td>
1188	<td>Genepix</td>
1189	</tr>
1190	<tr>
1191	<td>Platforms</td>
1192	<td>
1193	Generic<br>
1194	Affymetrix
1195	</td>
1196	</tr>
1197	<tr>
1198	<td>Array designs</td>
1199	<td>
1200	Array design A<br>
1201	Affymetrix A
1202	</td>
1203	</tr>
1204	<tr>
1205	<td>Protocols</td>
1206	<td>
1207	Sampling A<br>
1208	Extraction A<br>
1209	Labeling A<br>
1210	Library preparation A<br>
1211	Hybridization A<br>
1212	cBot Settings A<br>
1213	Scanning A<br>
1214	HiSeq Settings A<br>
1215	TopHat Settings A<br>
1216	Feature extraction A<br>
1217	Cufflinks Settings A<br>
1218	Printing A
1219	</td>
1220	</tr>
1221	<tr>
1222	<td>Hardware</td>
1223	<td>
1224	Hybridization station A<br>
1225	cBot A<br>
1226	HiSeq 2000 A<br>
1227	Scanner A<br>
1228	Print robot A
1229	</td>
1230	</tr>
1231	<tr>
1232	<td>Software</td>
1233	<td>
1234	Software A<br>
1235	TopHat<br>
1236	Cufflinks
1237	</td>
1238	</tr>
1239	</table>
1240
1241	<p>
1242	</li>
1243
1244	<li>
1245	Create array batches:
1246	<table class="listing" cellspacing="0" cellpadding="2" border="0">
1247	<tr>
1248	<th>Name</th>
1249	<th>Array design</th>
1250	<th>Print robot</th>
1251	<th>Protocol</th>
1252	</tr>
1253	<tr>
1254	<td>Array batch A</td>
1255	<td>Array design A</td>
1256	<td>Robot A</td>
1257	<td>Printing A</td>
1258	</tr>
1259	<tr>
1260	<td>Affymetrix batch A</td>
1261	<td>Affymetrix A</td>
1262	<td></td>
1263	<td></td>
1264	</tr>
1265	</table>
1266	<p>
1267	Or
1268	<p>
1269	Import array batches with the ArrayBatchImporter plug-in.
1270	<ol>
1271	<li>Click on the <code>Import</code> button on the array batch list page.</li>
1272	<li>Select ArrayBatchImporter in the plug-in drop-down list and click <code>Next</code></li>
1273	<li><b>Test with file:</b> <code>arraybatch_out.txt</code> and set the parsing parameters
1274	with help of the <code>Auto generate</code> button on the <code>Column mapping</code>
1275	tab.</li>
1276	<li>Start the import-job by clicking on the <code>Finish</code> button on the third wizzard-page.</li>
1277	</ol>
1278	<p>
1279	</li>
1280
1281	<li>
1282	Create array slides with the <code>Create slides</code>
1283	wizard.
1284
1285	<table class="listing" cellspacing="0" cellpadding="2" border="0">
1286	<tr>
1287	<th>Name</th>
1288	<th>Array batch</th>
1289	<th>Quantity</th>
1290	</tr>
1291	<tr>
1292	<td>Array slide A.</td>
1293	<td>Array batch A</td>
1294	<td>4</td>
1295	</tr>
1296	<tr>
1297	<td>Affymetrix slide A.</td>
1298	<td>Affymetrix batch A</td>
1299	<td>3</td>
1300	</tr>
1301	</table>
1302	<p>
1303	Or
1304	<p>
1305	Import array slides with the ArraySlideImporter plug-in.
1306	<ol>
1307	<li>Click on the <code>Import</code> button on the array slide list page.</li>
1308	<li>Select ArraySlideImporter in the plug-in drop-down list and click <code>Next</code></li>
1309	<li><b>Test with file:</b> <code>arrayslide_out.txt</code> and set the parsing parameters
1310	with help of the <code>Auto generate</code> button on the <code>Column mapping</code>
1311	tab.</li>
1312	<li>Start the import-job by clicking on the <code>Finish</code> button on the third wizzard-page.</li>
1313	</ol>
1314	<p>
1315	</li>
1316	</ol>
1317
1318	<a name="user"></a>
1319	<h2>5. User tests</h2>
1320	<p>
1321	The user is a typical worker in the project. The user does the actual experimentation in the
1322	lab, which includes collecting samples, doing extraction, labeling and hybridizations.
1323	The user also scans and analyses the raw data resulting from the images. Inserting items can be
1324	done in two different ways, .
1325	</p>
1326	<h3>First step</h3>
1327
1328	<ol>
1329	<li>Activate the <code>Project A</code> project.
1330	<p>
1331
1332	<li>
1333	Create a bioplate:
1334	<table class="listing" cellspacing="0" cellpadding="2" border="0">
1335	<tr>
1336	<th>Name</th>
1337	<th>Plate geometry</th>
1338	<th>Bioplate type</th>
1339	</tr>
1340	<tr>
1341	<td>Bioplate A</td>
1342	<td>96-well (8 x 12)</td>
1343	<td>BioPlate type A</td>
1344	</tr>
1345	</table>
1346	<p>
1347	<li>Continue with the second step, which can be done with batch importers or
1348	manually.
1349
1350	</ol>
1351
1352
1353	<h3>Second step (using batch importers)</h3>
1354
1355	<ol>
1356	<li>Click on the <code>Import</code> button on the list page.</li>
1357	<li>Select <itemtype>Importer in the plug-in drop-down list and click <code>Next</code></li>
1358	<li><b>Test with file:</b> using the right file(listed below) and set the parsing parameters
1359	by using the <code>Auto generate</code> button on the <code>Column mapping</code> tab.
1360	<table class="listing" cellspacing="0" cellpadding="2" border="0">
1361	<tr>
1362	<th>Itemtype</th>
1363	<th>File</th>
1364	</tr>
1365	<tr>
1366	<td>Biosource</td>
1367	<td>biosource_out.txt</td>
1368	</tr>
1369	<tr>
1370	<td>Samples</td>
1371	<td>sample_out.txt</td>
1372	</tr>
1373	<tr>
1374	<td>Extracts (including labeled extracts and libraries)</td>
1375	<td>extract_out.txt</td>
1376	</tr>
1377	<tr>
1378	<td>Physical bioassays (hybridizations, flow cells)</td>
1379	<td>physicalbioassay_out.txt</td>
1380	</tr>
1381	<tr>
1382	<td>Derived bioassays (scans, assemblys)</td>
1383	<td>derivedbioassay_out.txt</td>
1384	</tr>
1385	<tr>
1386	<td>Raw bioassays</td>
1387	<td>rawbioassay_out.txt</td>
1388	</tr>
1389	</table>
1390	The files listed for biosource, samples and derived bioassays also contain annotations
1391	for the items and these files should also be used with the annotation importer.
1392	The procedure is the same as for batch importers except that only <code>\Name\</code>
1393	is needed in the column mapping. The annotation column should be selected by default in
1394	the second wizard-step.
1395	</li>
1396	<li>Start the import-job by clicking on the <code>Finish</code> button on the third wizard-page.</li>
1397	<li>Continue with <a href="#step3">the third step</a>.</li>
1398	</ol>
1399
1400	<h3>Second step (create items manually)</h3>
1401	<ol>
1402	<li>
1403	Create a biosource:
1404	<table class="listing" cellspacing="0" cellpadding="2" border="0">
1405	<tr>
1406	<th>Name</th>
1407	<th>Annotations</th>
1408	</tr>
1409	<tr>
1410	<td>Biosource A</td>
1411	<td>
1412	<table border="0" cellspacing="0" cellpadding="2">
1413	<tr>
1414	<td><i>Drug resistance:</i></td>
1415	<td>medium</td>
1416	</tr>
1417	</table>
1418	</td>
1419	</tr>
1420	</table>
1421	<p>
1422	</li>
1423
1424	<li>
1425	Create samples:
1426	<table class="listing" cellspacing="0" cellpadding="2" border="0">
1427	<tr>
1428	<th>Name</th>
1429	<th>Protocol</th>
1430	<th>Biosource</th>
1431	<th>Bioplate [well]</th>
1432	<th>Annotations</th>
1433	</tr>
1434	<tr>
1435	<td>Sample A.00h</td>
1436	<td>Sampling A</td>
1437	<td>Biosource A</td>
1438	<td>Bioplate A [A1]</td>
1439	<td>
1440	<table border="0" cellspacing="0" cellpadding="2">
1441	<tr>
1442	<td><i>Time:</i></td>
1443	<td>0h</td>
1444	</tr>
1445	</table>
1446	</td>
1447	</tr>
1448	<tr>
1449	<td>Sample A.24h</td>
1450	<td>Sampling A</td>
1451	<td>Biosource A</td>
1452	<td>Bioplate A [A2]</td>
1453	<td>
1454	<table border="0" cellspacing="0" cellpadding="2">
1455	<tr>
1456	<td><i>Time:</i></td>
1457	<td>24h</td>
1458	</tr>
1459	</table>
1460	</td>
1461	</tr>
1462	<tr>
1463	<td>Sample A.ref</td>
1464	<td>Sampling A</td>
1465	<td>-</td>
1466	<td>Bioplate A [A3]</td>
1467	<td>-</td>
1468	</tr>
1469	</table>
1470	<p>
1471	</li>
1472
1473	<li>
1474	Create extracts:
1475	<table class="listing" cellspacing="0" cellpadding="2" border="0">
1476	<tr>
1477	<th>Name</th>
1478	<th>Protocol</th>
1479	<th>Sample</th>
1480	<th>Bioplate [well]</th>
1481	</tr>
1482	<tr>
1483	<td>Extract A.00h</td>
1484	<td>Extraction A</td>
1485	<td>Sample A.00h</td>
1486	<td>Bioplate A [B1]</td>
1487	</tr>
1488	<tr>
1489	<td>Extract A.24h</td>
1490	<td>Extraction A</td>
1491	<td>Sample A.24h</td>
1492	<td>Bioplate A [B2]</td>
1493	</tr>
1494	<tr>
1495	<td>Extract A.ref</td>
1496	<td>Extraction A</td>
1497	<td>Sample A.ref</td>
1498	<td>Bioplate A [B3]</td>
1499	</tr>
1500	</table>
1501	<p>
1502	</li>
1503
1504	<li>
1505	Create labeled extracts and libraries:
1506	<table class="listing" cellspacing="0" cellpadding="2" border="0">
1507	<tr>
1508	<th>Name</th>
1509	<th>Label</th>
1510	<th>Protocol</th>
1511	<th>Extract</th>
1512	<th>Bioplate [well]</th>
1513	</tr>
1514	<tr>
1515	<td>Labeled extract A.00h</td>
1516	<td>cy3</td>
1517	<td>Labeling A</td>
1518	<td>Extract A.00h</td>
1519	<td>Bioplate A [C1]</td>
1520	</tr>
1521	<tr>
1522	<td>Labeled extract A.24h</td>
1523	<td>cy3</td>
1524	<td>Labeling A</td>
1525	<td>Extract A.24h</td>
1526	<td>Bioplate A [C2]</td>
1527	</tr>
1528	<tr>
1529	<td>Labeled extract A.ref</td>
1530	<td>cy5</td>
1531	<td>Labeling A</td>
1532	<td>Extract A.ref</td>
1533	<td>Bioplate A [C3]</td>
1534	</tr>
1535	<tr class="shaded">
1536	<td>Labeled extract A.00h (dye-swap)</td>
1537	<td>cy5</td>
1538	<td>Labeling A</td>
1539	<td>Extract A.00h</td>
1540	<td>Bioplate A [D1]</td>
1541	</tr>
1542	<tr class="shaded">
1543	<td>Labeled extract A.24h (dye-swap)</td>
1544	<td>cy5</td>
1545	<td>Labeling A</td>
1546	<td>Extract A.24h</td>
1547	<td>Bioplate A [D2]</td>
1548	</tr>
1549	<tr class="shaded">
1550	<td>Labeled extract A.ref (dye-swap)</td>
1551	<td>cy3</td>
1552	<td>Labeling A</td>
1553	<td>Extract A.ref</td>
1554	<td>Bioplate A [D3]</td>
1555	</tr>
1556	<tr>
1557	<td>Library A.00h</td>
1558	<td>-</td>
1559	<td>Library preparation A</td>
1560	<td>Extract A.00h</td>
1561	<td>Bioplate A [E1]</td>
1562	</tr>
1563	<tr>
1564	<td>Library A.24h</td>
1565	<td>-</td>
1566	<td>Library preparation A</td>
1567	<td>Extract A.24h</td>
1568	<td>Bioplate A [E2]</td>
1569	</tr>
1570	<tr>
1571	<td>Library A.ref</td>
1572	<td>-</td>
1573	<td>Library preparation A</td>
1574	<td>Extract A.ref</td>
1575	<td>Bioplate A [E3]</td>
1576	</tr>
1577	</table>
1578	<p>
1579	</li>
1580
1581	<li>
1582	Create physical bioassays (hybridizations and flow cells):
1583	<table class="listing" cellspacing="0" cellpadding="2" border="0">
1584	<tr>
1585	<th>Name</th>
1586	<th>Protocol</th>
1587	<th>Hardware</th>
1588	<th>Array slide</th>
1589	<th>Extracts (position)</th>
1590	</tr>
1591	<tr>
1592	<td>Hybridization A.00h</td>
1593	<td>Hybridization A</td>
1594	<td>Hybridization station A</td>
1595	<td>Array slide A.1</td>
1596	<td>Labeled extract A.00h,<br>Labeled extract A.ref</td>
1597	</tr>
1598	<tr>
1599	<td>Hybridization A.24h</td>
1600	<td>Hybridization A</td>
1601	<td>Hybridization station A</td>
1602	<td>Array slide A.2</td>
1603	<td>Labeled extract A.24h,<br>Labeled extract A.ref</td>
1604	</tr>
1605	<tr class="shaded">
1606	<td>Hybridization A.00h (dye-swap)</td>
1607	<td>Hybridization A</td>
1608	<td>Hybridization station A</td>
1609	<td>Array slide A.3</td>
1610	<td>Labeled extract A.00h (dye-swap),<br>Labeled extract A.ref (dye-swap)</td>
1611	</tr>
1612	<tr class="shaded">
1613	<td>Hybridization A.24h (dye-swap)</td>
1614	<td>Hybridization A</td>
1615	<td>Hybridization station A</td>
1616	<td>Array slide A.4</td>
1617	<td>Labeled extract A.24h (dye-swap),<br>Labeled extract A.ref (dye-swap)</td>
1618	</tr>
1619	<tr>
1620	<td>Affymetrix hyb A.1</td>
1621	<td>Hybridization A</td>
1622	<td>Hybridization station A</td>
1623	<td>Affymetrix slide A.1</td>
1624	<td>Labeled extract A.00h</td>
1625	</tr>
1626	<tr>
1627	<td>Affymetrix hyb A.2</td>
1628	<td>Hybridization A</td>
1629	<td>Hybridization station A</td>
1630	<td>Affymetrix slide A.2</td>
1631	<td>Labeled extract A.24h</td>
1632	</tr>
1633	<tr>
1634	<td>Affymetrix hyb A.3</td>
1635	<td>Hybridization A</td>
1636	<td>Hybridization station A</td>
1637	<td>Affymetrix slide A.3</td>
1638	<td>Labeled extract A.ref</td>
1639	</tr>
1640	<tr class="shaded">
1641	<td>Flow cell A</td>
1642	<td>cBot Settings A</td>
1643	<td>cBot A</td>
1644	<td>-</td>
1645	<td>Library A.00h (1),<br>Library A.24h (2)<br>Library A.ref (3)</td>
1646	</tr>
1647	</table>
1648	<p>
1649	</li>
1650
1651	<li>
1652	Create derived bioassays (scans, assemblys, etc.):
1653	<table class="listing" cellspacing="0" cellpadding="2" border="0">
1654	<tr>
1655	<th>Name</th>
1656	<th>Parent bioasasay</th>
1657	<th>Parent extract</th>
1658	<th>Hardware/Software</th>
1659	<th>Protocol</th>
1660	<th>PMT gain</th>
1661	</tr>
1662	<tr>
1663	<td>Scan A.00h</td>
1664	<td>Hybridization A.00h</td>
1665	<td>Labeled extract A.00h</td>
1666	<td>HW: Scanner A</td>
1667	<td>Scanning A</td>
1668	<td>400 V</td>
1669	</tr>
1670	<tr>
1671	<td>Scan A.24h</td>
1672	<td>Hybridization A.24h</td>
1673	<td>Labeled extract A.24h</td>
1674	<td>HW: Scanner A</td>
1675	<td>Scanning A</td>
1676	<td>500 V</td>
1677	</tr>
1678	<tr class="shaded">
1679	<td>Scan A.00h (dye-swap)</td>
1680	<td>Hybridization A.00h (dye-swap)</td>
1681	<td>Labeled extract A.00h (dye-swap)</td>
1682	<td>HW: Scanner A</td>
1683	<td>Scanning A</td>
1684	<td>600 V</td>
1685	</tr>
1686	<tr class="shaded">
1687	<td>Scan A.24h (dye-swap)</td>
1688	<td>Hybridization A.24h (dye-swap)</td>
1689	<td>Labeled extract A.24h (dye-swap)</td>
1690	<td>HW: Scanner A</td>
1691	<td>Scanning A</td>
1692	<td>700 V</td>
1693	</tr>
1694	<tr>
1695	<td>Affymetrix scan A.1</td>
1696	<td>Affymetrix hyb A.1</td>
1697	<td>Labeled extract A.00h</td>
1698	<td>HW: Scanner A</td>
1699	<td>Scanning A</td>
1700	<td>800 V</td>
1701	</tr>
1702	<tr>
1703	<td>Affymetrix scan A.2</td>
1704	<td>Affymetrix hyb A.2</td>
1705	<td>Labeled extract A.24h</td>
1706	<td>HW: Scanner A</td>
1707	<td>Scanning A</td>
1708	<td>900 V</td>
1709	</tr>
1710	<tr>
1711	<td>Affymetrix scan A.3</td>
1712	<td>Affymetrix hyb A.3</td>
1713	<td>Labeled extract A.ref</td>
1714	<td>HW: Scanner A</td>
1715	<td>Scanning A</td>
1716	<td>1000 V</td>
1717	</tr>
1718	<tr class="shaded">
1719	<td>Sequenced A</td>
1720	<td>Flow cell A</td>
1721	<td>-</td>
1722	<td>HW: HiSeq 2000 A</td>
1723	<td>HiSeq Settings A</td>
1724	<td>-</td>
1725	</tr>
1726	<tr class="shaded">
1727	<td>Assembly A.00h</td>
1728	<td>Sequenced A</td>
1729	<td>Library A.00h</td>
1730	<td>SW: TopHat</td>
1731	<td>TopHat Settings A</td>
1732	<td>-</td>
1733	</tr>
1734	<tr class="shaded">
1735	<td>Assembly A.24h</td>
1736	<td>Sequenced A</td>
1737	<td>Library A.24h</td>
1738	<td>SW: TopHat</td>
1739	<td>TopHat Settings A</td>
1740	<td>-</td>
1741	</tr>
1742	<tr class="shaded">
1743	<td>Assembly A.ref</td>
1744	<td>Sequenced A</td>
1745	<td>Library A.ref</td>
1746	<td>SW: TopHat</td>
1747	<td>TopHat Settings A</td>
1748	<td>-</td>
1749	</tr>
1750	</table>
1751	<p>
1752	</li>
1753
1754	<li>
1755	Add data files (TODO - we don't have any yet):
1756	<table class="listing" cellspacing="0" cellpadding="2" border="0">
1757	<tr>
1758	<th>Scan</th>
1759	<th>Data files</th>
1760	</tr>
1761	<tr>
1762	<td>Scan A.00h</td>
1763	<td>-</td>
1764	</tr>
1765	<tr>
1766	<td>Scan A.24h</td>
1767	<td>-</td>
1768	</tr>
1769	<tr class="shaded">
1770	<td>Scan A.00h (dye-swap)</td>
1771	<td>-</td>
1772	</tr>
1773	<tr class="shaded">
1774	<td>Scan A.24h (dye-swap)</td>
1775	<td>-</td>
1776	</tr>
1777	</table>
1778	<p>
1779	</li>
1780
1781	<li>
1782	Create raw bioassays:
1783	<table class="listing" cellspacing="0" cellpadding="2" border="0">
1784	<tr>
1785	<th>Name</th>
1786	<th>Platform/Raw data type</th>
1787	<th>Parent bioassay</th>
1788	<th>Parent extract</th>
1789	<th>Array design</th>
1790	<th>Protocol</th>
1791	<th>Software</th>
1792	<th>File(s)</th>
1793	</tr>
1794	<tr>
1795	<td>Raw bioassay A.00h</td>
1796	<td>Generic/GenePix</td>
1797	<td>Scan A.00h</td>
1798	<td>Labeled extract A.00h</td>
1799	<td>Array design A</td>
1800	<td>Feature extraction A</td>
1801	<td>Software A</td>
1802	<td><i>Raw data</i>: genepix.mouse.v4.37k.00h.gpr</td>
1803	</tr>
1804	<tr>
1805	<td>Raw bioassay A.24h</td>
1806	<td>Generic/GenePix</td>
1807	<td>Scan A.24h</td>
1808	<td>Labeled extract A.24h</td>
1809	<td>Array design A</td>
1810	<td>Feature extraction A</td>
1811	<td>Software A</td>
1812	<td><i>Raw data</i>: genepix.mouse.v4.37k.24h.gpr</td>
1813	</tr>
1814	<tr class="shaded">
1815	<td>Raw bioassay A.00h (dye-swap)</td>
1816	<td>Generic/GenePix</td>
1817	<td>Scan A.00h (dye-swap)</td>
1818	<td>Labeled extract A.00h (dye-swap)</td>
1819	<td>Array design A</td>
1820	<td>Feature extraction A</td>
1821	<td>Software A</td>
1822	<td><i>Raw data</i>: genepix.mouse.v4.37k.00h.dyeswap.gpr</td>
1823	</tr>
1824	<tr class="shaded">
1825	<td>Raw bioassay A.24h (dye-swap)</td>
1826	<td>Generic/GenePix</td>
1827	<td>Scan A.24h (dye-swap)</td>
1828	<td>Labeled extract A.24h (dye-swap)</td>
1829	<td>Array design A</td>
1830	<td>Feature extraction A</td>
1831	<td>Software A</td>
1832	<td><i>Raw data</i>: genepix.mouse.v4.37k.24h.dyeswap.gpr</td>
1833	</tr>
1834	<tr>
1835	<td>Affymetrix raw A.1</td>
1836	<td>Affymetrix</td>
1837	<td>Affymetrix scan A.1</td>
1838	<td>Labeled extract A.00h</td>
1839	<td>Affymetrix A</td>
1840	<td>Feature extraction A</td>
1841	<td>Software A</td>
1842	<td><i>CEL file</i>: jos1761.cel.bz2</td>
1843	</tr>
1844	<tr>
1845	<td>Affymetrix raw A.2</td>
1846	<td>Affymetrix</td>
1847	<td>Affymetrix scan A.2</td>
1848	<td>Labeled extract A.24h</td>
1849	<td>Affymetrix A</td>
1850	<td>Feature extraction A</td>
1851	<td>Software A</td>
1852	<td><i>CEL file</i>: jos1762.cel.bz2</td>
1853	</tr>
1854	<tr>
1855	<td>Affymetrix raw A.3</td>
1856	<td>Affymetrix</td>
1857	<td>Affymetrix scan A.3</td>
1858	<td>Labeled extract A.ref</td>
1859	<td>Affymetrix A</td>
1860	<td>Feature extraction A</td>
1861	<td>Software A</td>
1862	<td><i>CEL file</i>: jos1763.cel.bz2</td>
1863	</tr>
1864	<tr class="shaded">
1865	<td>SeqRaw A.00h</td>
1866	<td>Generic/GenePix</td>
1867	<td>Assembly A.00h</td>
1868	<td>Library A.00h</td>
1869	<td>Array design A</td>
1870	<td>Cufflinks Settings A</td>
1871	<td>Cufflinks</td>
1872	<td></td>
1873	</tr>
1874	<tr class="shaded">
1875	<td>SeqRaw A.24h</td>
1876	<td>Generic/GenePix</td>
1877	<td>Assembly A.24h</td>
1878	<td>Library A.24h</td>
1879	<td>Array design A</td>
1880	<td>Cufflinks Settings A</td>
1881	<td>Cufflinks</td>
1882	<td></td>
1883	</tr>
1884	<tr class="shaded">
1885	<td>SeqRaw A.ref</td>
1886	<td>Generic/GenePix</td>
1887	<td>Assembly A.ref</td>
1888	<td>Library A.ref</td>
1889	<td>Array design A</td>
1890	<td>Cufflinks Settings A</td>
1891	<td>Cufflinks</td>
1892	<td></td>
1893	</tr>
1894	</table>
1895	TODO - create other raw data type for sequence raw bioassays
1896	<p>
1897	</li>
1898	</ol>
1899
1900	<a name="step3"></a>
1901	<h3>Third step</h3>
1902	<ol>
1903	<li>
1904	Create experiments:
1905	<table class="listing" cellspacing="0" cellpadding="2" border="0">
1906	<tr>
1907	<th>Name</th>
1908	<th>Raw data type</th>
1909	<th>Raw bioassays</th>
1910	<th>Experimental factors</th>
1911	</tr>
1912	<tr>
1913	<td>Experiment A</td>
1914	<td>GenePix</td>
1915	<td>Raw bioassay A.00h,<br>Raw bioassay A.24h,<br>Raw bioassay A.00h (dye-swap),<br>
1916	Raw bioassay A.24h (dye-swap)</td>
1917	<td>Drug resistance, Time, Dye swap, PMT gain</td>
1918	</tr>
1919	<tr>
1920	<td>Affymetrix A</td>
1921	<td>Affymetrix</td>
1922	<td>Affymetrix raw A.1,<br>Affymetrix raw A.2,<br>Affymetrix raw A.3</td>
1923	<td>Drug resistance, Time, PMT gain</td>
1924	</tr>
1925	<tr>
1926	<td>Sequence A</td>
1927	<td>GenePix</td>
1928	<td>SeqRaw A.00h,<br>SeqRaw A.24h,<br>SeqRaw A.ref</td>
1929	<td>Drug resistance, Time</td>
1930	</tr>
1931	</table>
1932	<p>
1933	</li>
1934
1935	<li><a name="inheritannotations"></a>
1936	Inherit the annotations from the scans, samples and biosource for each raw bioassay.
1937	Use the <i>auto-inherit</i> function that exists on the experiment properties
1938	tab. Make sure that all experimental factors are selected by the check boxes,
1939	then click on the <i>Auto-inherit</i> link in the column header.
1940	Note! The <i>Dye swap</i>
1941	annotation will not get values until the next step, and the <i>Affymetrix raw A.3</i>
1942	data set is missing biomaterial parents with annotations.
1943	<p>
1944
1945	</li>
1946
1947	<li>
1948	Import GenePix raw data. There are two possible ways to do this:
1949	<ol>
1950	<li>Manually import to each raw bioassay.
1951	<li>Batch import to multiple raw bioassays.
1952	</ol>
1953	<p>
1954	<b>Manual import:</b> Go to the properties tab for each raw bioassay.
1955	Click on the <i>Import</i> button and use the auto-detect feature to
1956	import the raw data. Use the default configuration values except for
1957	those listed in the table below.
1958	<p>
1959
1960	<b>Batch import:</b> The batch import is started from the
1961	properties tab of the <i>experiment</i>. Click on "Import" and
1962	use the auto-detect feature with one of the used files. Use the default
1963	configuration values except for those listed in the table below.
1964	The batch import should import two raw data sets in one go (since it can
1965	only work with a single file format at a time and the dye-swap files uses
1966	a different file format). Repeat the batch import a second time to import
1967	the remaining two raw data sets.
1968	<p>
1969
1970	<table class="listing" cellspacing="0" cellpadding="2" border="0">
1971	<tr>
1972	<th>Parameter</th>
1973	<th>Value</th>
1974	<th>Mode</th>
1975	</tr>
1976	<tr>
1977	<td>Feature mismatch</td>
1978	<td>smart</td>
1979	<td>both</td>
1980	</tr>
1981	<tr>
1982	<td>Invalid numeric value</td>
1983	<td>null</td>
1984	<td>both</td>
1985	</tr>
1986	<tr>
1987	<td>Log file</td>
1988	<td>~/import.log</td>
1989	<td>batch import</td>
1990	</tr>
1991	</table>
1992	<p>
1993
1994	In both cases, the import should produce the same results
1995	as in the table below. When using the batch import mode, the
1996	detailed information for each raw bioassay is only found in
1997	the log file.
1998	<table class="listing" cellspacing="0" cellpadding="2" border="0">
1999	<tr>
2000	<th>Raw bioassay</th>
2001	<th>Raw data file</th>
2002	<th>Spots inserted/with null reporter/skipped)</th>
2003	<th>Annotations created</th>
2004	</tr>
2005	<tr>
2006	<td>Raw bioassay A.00h</td>
2007	<td>genepix.mouse.v4.37k.00h.gpr</td>
2008	<td>36,864/632/768</td>
2009	<td><i>Dye swap</i>: false</td>
2010	</tr>
2011	<tr>
2012	<td>Raw bioassay A.24h</td>
2013	<td>genepix.mouse.v4.37k.24h.gpr</td>
2014	<td>36,864/632/768</td>
2015	<td><i>Dye swap</i>: false</td>
2016	</tr>
2017	<tr class="shaded">
2018	<td>Raw bioassay A.00h (dye-swap)</td>
2019	<td>genepix.mouse.v4.37k.00h.dyeswap.gpr</td>
2020	<td>36,864/632/768</td>
2021	<td><i>Dye swap</i>: true</td>
2022	</tr>
2023	<tr class="shaded">
2024	<td>Raw bioassay A.24h (dye-swap)</td>
2025	<td>genepix.mouse.v4.37k.24h.dyeswap.gpr</td>
2026	<td>36,864/632/768</td>
2027	<td><i>Dye swap</i>: true</td>
2028	</tr>
2029	</table>
2030	<p>
2031
2032	</li>
2033
2034	<li>
2035	Check the experiment overview page. It should display one warnings for the
2036	Genepix experiment. The warning is related to a missing biosurce
2037	on the reference sample.
2038	<p>
2039	The Affymetrix experiment gives some more warnings. Most of them are
2040	related to not using the project default items, missing protocols
2041	and missing hardware. There should also be an error about missing
2042	experimental factor values for the <code>Affymetrix.3</code>
2043	raw bioassay. It is expected since this comes from the reference sample
2044	which doesn't have values for those annotations.
2045	<p>
2046
2047	Change validation options to reduce the number of warnings:
2048	<table class="listing" cellspacing="0" cellpadding="2" border="0">
2049	<tr>
2050	<th>Validation option</th>
2051	<th>Setting</th>
2052	</tr>
2053	<tr>
2054	<td>Project defaults</td>
2055	<td>Set all to <code>Ignore</code></td>
2056	</tr>
2057	<tr>
2058	<td>Missing items</td>
2059	<td>Set all to <code>Ignore</code></td>
2060	</tr>
2061	<tr>
2062	<td>Annotations - Missing factor value</td>
2063	<td><code>Warning</code></td>
2064	</tr>
2065	<tr>
2066	<td>Other - Raw spots <> features</td>
2067	<td><code>Ignore</code></td>
2068	</tr>
2069	</table>
2070
2071	After the changes there should now only be two warnings about the
2072	missing factor values.
2073
2074	<p>
2075	</li>
2076
2077	</ol>
2078	</li>
2079	</ol>
2080
2081	<a name="analysis"></a>
2082	<h2>6. Analysis tests</h2>
2083	<p>
2084	Now it is time to analyse the data. The analysis test should be done
2085	by both a regular user and a guest.
2086	</p>
2087
2088	<ol>
2089	<li>
2090	Activate the <code>Project A</code> project<p>
2091	</li>
2092
2093	<li>
2094	Go to the <code>Experiment A</code> experiment and select
2095	the <code>Bioassay sets</code> tab.
2096	<p>
2097	</li>
2098
2099	<li>
2100	Create a new root bioassay set:
2101	<table class="listing" cellspacing="0" cellpadding="2" border="0">
2102	<tr>
2103	<th>Bioassay set name</th>
2104	<th>Raw bioassays</th>
2105	<th>Formula</th>
2106	</tr>
2107	<tr>
2108	<td>Root bioassay set</td>
2109	<td>all</td>
2110	<td>Mean FG - Mean BG</td>
2111	</tr>
2112	</table>
2113	Wait for the plug-in to finish.
2114	<p>
2115	</li>
2116
2117	<li>
2118	Select the created bioassay set and create a filtered bioassayset:
2119	<table class="listing" cellspacing="0" cellpadding="2" border="0">
2120	<tr>
2121	<th>Child name</th>
2122	<th>Filter preset</th>
2123	<th>Expression</th>
2124	</tr>
2125	<tr>
2126	<td>Filtered bioassay set</td>
2127	<td>-</td>
2128	<td>ch(1) > 0 && ch(2) > 0 && rep('id') != null</td>
2129	</tr>
2130	</table>
2131	Wait for the plug-in to finish. It should report that 136,498 spots remain and
2132	that 10,958 spots has been removed.
2133	<p>
2134	</li>
2135
2136	<li>
2137	Select the filtered bioassay set and run a normalization plug-in:
2138	<table class="listing" cellspacing="0" cellpadding="2" border="0">
2139	<tr>
2140	<th>Plugin</th>
2141	<th>Parameters</th>
2142	</tr>
2143	<tr>
2144	<td>Normalization: Lowess</td>
2145	<td>Accept the default parameters.</td>
2146	</tr>
2147	</table>
2148	Wait for the plug in to finish. It should report that 136,498 spots has been
2149	normalized and 0 spots has been removed.
2150	<p>
2151	</li>
2152
2153	<li>
2154	Select the normalized bioassay set and check the MA plots and
2155	the correction factor plots. Here are four examples:
2156	<table class="listing" cellspacing="0" cellpadding="2" border="0">
2157	<tr>
2158	<th>MA plots</th>
2159	<th>Correction factor plots</th>
2160	</tr>
2161	<tr>
2162	<td><img src="overview.png"><br><img src="overview.dyeswap.png"></td>
2163	<td><img src="correction.png"><br><img src="correction.dyeswap.png"></td>
2164	</tr>
2165	</table>
2166	<p>
2167	</li>
2168
2169	<li>
2170	Try the plot tool with the following plots. Use the <code>Save</code> function
2171	to save one them as a file in the BASE file system, and the <code>Download</code>
2172	function to download a plot to your computer.
2173	<table class="listing" cellspacing="0" cellpadding="2" border="0">
2174	<tr>
2175	<th>Plot type</th>
2176	<th>Y-axis preset</th>
2177	<th>X-axis preset</th>
2178	<th>Other options</th>
2179	</tr>
2180	<tr>
2181	<td>Scatter plot</td>
2182	<td>M, log2(ch1 / ch2)</td>
2183	<td>A, log10(ch1 * ch2) / 2</td>
2184	<td>-</td>
2185	</tr>
2186	<tr>
2187	<td>Histogram plot</td>
2188	<td>Count</td>
2189	<td>Ratio, ch1 / ch2</td>
2190	<td>
2191	<table border="0" cellspacing="0" cellpadding="2">
2192	<tr>
2193	<td><i>Log scale</i></td>
2194	<td>checked</td>
2195	</tr>
2196	<tr>
2197	<td><i>Bin size</i></td>
2198	<td>0.1</td>
2199	</tr>
2200	<tr>
2201	<td><i>Annotation</i></td>
2202	<td>Time</td>
2203	</tr>
2204	</table>
2205	</td>
2206	</tr>
2207	</table>
2208	<p>
2209	Here are two examples:
2210	<table class="listing" cellspacing="0" cellpadding="2" border="0">
2211	<tr>
2212	<th>Scatter plot</th>
2213	</tr>
2214	<tr>
2215	<td><img src="scatter.png"></td>
2216	</tr>
2217	</table>
2218	<p>
2219	<table class="listing" cellspacing="0" cellpadding="2" border="0">
2220	<tr>
2221	<th>Histogram plot</th>
2222	</tr>
2223	<tr>
2224	<td><img src="histogram.png"></td>
2225	</tr>
2226	</table>
2227	<p>
2228	</li>
2229
2230	</ol>
2231
2232
2233	</body>
2234	</html>

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