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Last change on this file since 4626 was 4626, checked in by Nicklas Nordborg, 15 years ago

Fixes #1164: Reporter importer plug-in displays 'Reporter ID' when setting column mappings... should be 'External ID'

Decided to keep 'Reporter ID' on other plug-ins and only calrify the description since if using 'External ID' it is not clear what this references (eg. spot external id, feature external id...)

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

File size: 41.4 KB

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3	$Id: index.html 4626 2008-11-05 09:56:12Z nicklas $
4
5	Copyright (C) 2006 Jari Hakkinen, Nicklas Nordborg, Martin Svensson
6
7	This file is part of BASE - BioArray Software Environment.
8	Available at http://base.thep.lu.se/
9
10	BASE is free software; you can redistribute it and/or
11	modify it under the terms of the GNU General Public License
12	as published by the Free Software Foundation; either version 3
13	of the License, or (at your option) any later version.
14
15	BASE is distributed in the hope that it will be useful,
16	but WITHOUT ANY WARRANTY; without even the implied warranty of
17	MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
18	GNU General Public License for more details.
19
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21	along with BASE. If not, see <http://www.gnu.org/licenses/>.
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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="../../styles.css">
27	</head>
28	<body>
29
30	<div class="navigation">
31	<a href="../../index.html">BASE</a>
32	<img src="../../next.gif">
33	<a href="../index.html">Test procedures</a>
34	<img src="../../next.gif">
35	Predefined roles
36	</div>
37
38	<h1>Test procedures for predefined roles</h1>
39
40	<div class="abstract">
41	<p>
42	This document defines a procedure for testing that
43	the predefined roles can perform their work as intended. The main
44	purpose is to weed out permission problems resulting from:
45	</p>
46
47	<ul>
48	<li>Incorrect permissions installed by installation program</li>
49	<li>Bugs in the permission handling in the core</li>
50	<li>Incorrect handling of permissions in the web client</li>
51	</ul>
52
53	<p>
54	The test procedure also tests that the
55	basic functionality is working:
56	</p>
57
58	<ul>
59	<li>Creating items and linking them to other items</li>
60	<li>Defining import file formats</li>
61	<li>Importing array LIMS data</li>
62	<li>Importing and validating raw data against array LIMS data</li>
63	<li>Running analysis plug-ins</li>
64	<li>Using files instead of the database for storing data</li>
65	</ul>
66
67	<b>Contents</b><br>
68	<ol>
69	<li><a href="#summary">Summary of the test procedure</a></li>
70	<li><a href="#root">Root user tests</a></li>
71	<li><a href="#admin">Administrator tests</a></li>
72	<li><a href="#power">Power user tests</a></li>
73	<li><a href="#user">User tests</a></li>
74	<li><a href="#analysis">Analysis tests</a></li>
75	</ol>
76
77	<p class="authors">
78	<b>Last updated:</b> $Date: 2008-11-05 09:56:12 +0000 (Wed, 05 Nov 2008) $
79	</p>
80	</div>
81
82
83	<a name="summary"></a>
84	<h2>1. Summary of the test procedure</h2>
85
86	<p>
87	Here is a summary of the test procedure:
88	</p>
89
90	<ol>
91	<li>Always start with a fresh installation.</li>
92
93	<li>The root user creates an administrator.</li>
94
95	<li>The administrator creates more users and some global resources:
96	<ul>
97	<li>A group and three other users. One power user, one user and one guest.</li>
98	<li>File formats for importing reporters</li>
99	<li>Imports reporters</li>
100	</ul>
101	</li>
102
103	<li>The power user creates item related to the project management:
104	<ul>
105	<li>A project</li>
106	<li>Protocols, one for each type of action: sampling, extraction, etc.</li>
107	<li>Hardware and software that are used in the project</li>
108	<li>Annotation types for annotations used in the project</li>
109	<li>File formats for importing plates, print maps and raw data</li>
110	<li>LIMS information - plate type, plates, array design, array batch and array slides</li>
111	</ul>
112	</li>
113
114	<li>The user creates items related to an actual experiment:
115	<ul>
116	<li>Biomaterials: biosources, samples, extracts, etc.</li>
117	<li>Experiment: hybridizations, scans, images, raw bioassays</li>
118	<li>Import raw data</li>
119	</ul>
120	</li>
121
122	<li>Both the user and the guest then do some analysis:
123	<ul>
124	<li>Create a root bioassay set</li>
125	<li>Filter the bioassay set</li>
126	<li>Run a normalization plug-in</li>
127	<li>Check the result by listing and plotting the data</li>
128	</ul>
129	</li>
130	</ol>
131
132	<p>
133	These tests can also be run in automated mode by test programs. This will of
134	course not test the web client, but are useful if one quickly needs to do
135	parts of the test and then continue with, for example, the user or analysis tests
136	on the web.
137	</p>
138
139	<p>
140	The data files needed by the tests are NOT included in the subversion repository.
141	The main reason is that they are too large, and that we don't have permission to
142	make them publicly available for download. To get the test file you need to be a
143	core developer. Read the instructions on the
144	<a href="http://base.thep.lu.se/wiki/DeveloperInformation">DeveloperInformation</a>
145	page, <code>Test data</code> section on the Base 2 web site. The automated
146	test programs require that file are placed (checked out) in the 'testdata'
147	directory located in the BASE root directory. NOTE! Some test data files are
148	bzip-compressed. These need to be uncompressed before they are uploaded to BASE.
149	</p>
150
151	<p>
152	To run the tests do the following:
153	</p>
154	<ol>
155
156	<li>Compile the core and the test programs: <code>ant main test</code>.</li>
157
158	<li>Change to the <code>build/test/</code> directory.</li>
159
160	<li>Run test programs: <code>./test.sh roles <cmds></code> where
161	<code><cmds></code> is one or more of the following:
162	<ul>
163	<li><code>all</code>: run all tests</li>
164	<li><code>root</code>: run the root user tests</li>
165	<li><code>admin</code>: run the administrator tests</li>
166	<li><code>power</code>: run the power user tests</li>
167	<li><code>user</code>: run the regular user tests</li>
168	<li><code>guest</code>: run the guest user tests</li>
169	</ul>
170	</li>
171
172	</ol>
173
174	<a name="root"></a>
175	<h2>2. Root user tests</h2>
176	<p>
177	The root user creates an administrator which is a server-wide admin.
178	</p>
179
180	<ol>
181	<li>
182	Create a new user and set the following
183	properties. All other properties may remain unchanged.
184
185	<table class="listing" cellspacing="0" cellpadding="2" border="0">
186	<tr>
187	<th>Name</th>
188	<th>Login/Password</th>
189	<th>Quota</th>
190	<th>Quota group</th>
191	<th>Membership</th>
192	</tr>
193	<tr>
194	<td>Admin</td>
195	<td>admin/admin</td>
196	<td>Unlimited</td>
197	<td>-</td>
198	<td>Roles: Administrator</td>
199	</tr>
200	</table>
201	</li>
202	</ol>
203
204	<a name="admin"></a>
205	<h2>3. Administrator tests</h2>
206	<p>
207	The administrator creates users for a project and gives them permissions
208	that are suitable for their role in the project. The administrator also
209	sets up quota and group membership.
210	</p>
211
212	<ol>
213	<li>
214	Create a new group and set the following properties:
215
216	<table class="listing" cellspacing="0" cellpadding="2" border="0">
217	<tr>
218	<th>Name</th>
219	<th>Quota</th>
220	</tr>
221	<tr>
222	<td>Group A</td>
223	<td>1GB</td>
224	</tr>
225	</table>
226	<p>
227	</li>
228
229	<li>
230	Create the following users:
231
232	<table class="listing" cellspacing="0" cellpadding="2" border="0">
233	<tr>
234	<th>Name</th>
235	<th>Login/Password</th>
236	<th>Quota</th>
237	<th>Quota group</th>
238	<th>Membership</th>
239	<th>Other</th>
240	</tr>
241	<tr>
242	<td>Power user</td>
243	<td>power/power</td>
244	<td>1GB</td>
245	<td>Group A</td>
246	<td>Roles: Power user</td>
247	<td>-</td>
248	</tr>
249	<tr>
250	<td>User</td>
251	<td>user/user</td>
252	<td>1GB</td>
253	<td>Group A</td>
254	<td>Roles: User</td>
255	<td>-</td>
256	</tr>
257	<tr>
258	<td>Guest</td>
259	<td>guest/guest</td>
260	<td>10MB</td>
261	<td>Group A</td>
262	<td>Roles: Guest</td>
263	<td><i>Multi-user account</i> checked</td>
264	</tr>
265	</table>
266	<p>
267	</li>
268
269	<li>Give USE permission for the listed users to the following plugins:
270
271	<table class="listing" cellspacing="0" cellpadding="2" border="0">
272	<tr>
273	<th>User</th>
274	<th>Plugins</th>
275	</tr>
276	<tr>
277	<td>Power user</td>
278	<td>
279	<ul>
280	<li>Plate importer</li>
281	<li>Reporter map importer</li>
282	<li>Print map importer</li>
283	</ul>
284	</td>
285	</tr>
286	</table>
287	<p>
288	</li>
289
290	<li>
291	Create file formats (<i>i.e.</i>, plug-in configurations) for importing
292	reporters. The formats marked as
293	optional are not used in the test procedure, but may be useful to weed
294	out import problems, since they allow importing all info from the raw
295	data files. You may either enter the regular expressions as specified or
296	use the "Test with file" feature.
297
298	<table class="listing" cellspacing="0" cellpadding="2" border="0">
299	<tr>
300	<th>Name</th>
301	<th>Plugin</th>
302	<th>Configuration values</th>
303	</tr>
304	<tr class="oddrow">
305	<td>Reporters for project A</td>
306	<td>Reporter importer</td>
307	<td>
308	<b>Test with file:</b> <code>plates_and_reporters.mouse.v4.37k.txt</code>
309	<table border="0" cellspacing="0" cellpadding="2">
310	<tr>
311	<td><i>Data header</i></td>
312	<td>384_number\t384_column\t384_row\t384_position\toligo_id.*</td>
313	</tr>
314	<tr>
315	<td><i>Data splitter</i></td>
316	<td>\t</td>
317	</tr>
318	<tr>
319	<td><i>Min data columns</i></td>
320	<td>5</td>
321	</tr>
322	<tr>
323	<td><i>Name</i></td>
324	<td>\oligo_id\</td>
325	</tr>
326	<tr>
327	<td><i>External ID</i></td>
328	<td>\oligo_id\</td>
329	</tr>
330	<tr>
331	<td><i>Description</i></td>
332	<td>\description_Ensembl*\</td>
333	</tr>
334	<tr>
335	<td><i>Gene symbol</i></td>
336	<td>\gene_symbol_Ensembl*\</td>
337	</tr>
338	<tr>
339	<td><i>Sequence</i></td>
340	<td>\oligo_sequence\</td>
341	</tr>
342	</table>
343
344	</td>
345	</tr>
346
347	<tr class="evenrow">
348	<td>GenePix reporter importer<br>(optional)</td>
349	<td>Reporter importer</td>
350	<td>
351
352	<b>Test with file:</b> <code>genepix.mouse.v4.37k.00h.gpr</code>
353	<table border="0" cellspacing="0" cellpadding="2">
354	<tr>
355	<td><i>Data header</i></td>
356	<td>"Block"\t"Column"\t"Row"\t"Name"\t"ID"\t.*</td>
357	</tr>
358	<tr>
359	<td><i>Data splitter</i></td>
360	<td>\t</td>
361	</tr>
362	<tr>
363	<td><i>Min data columns</i></td>
364	<td>48</td>
365	</tr>
366	<tr>
367	<td><i>Max data columns</i></td>
368	<td>48</td>
369	</tr>
370	<tr>
371	<td><i>Name</i></td>
372	<td>\Name\</td>
373	</tr>
374	<tr>
375	<td><i>External ID</i></td>
376	<td>\ID\</td>
377	</tr>
378	</table>
379
380	</td>
381	</tr>
382	<tr class="oddrow">
383	<td>Reporters from Affymetrix annotations file</td>
384	<td>Reporter importer</td>
385	<td>
386	<b>Test with file:</b> <code>MG_U74Av2_annot.csv.bz2</code>
387	<table border="0" cellspacing="0" cellpadding="2">
388	<tr>
389	<td><i>Data header</i></td>
390	<td>"Probe Set ID","GeneChip Array".*</td>
391	</tr>
392	<tr>
393	<td><i>Data splitter</i></td>
394	<td>(?!"),(?=")</td>
395	</tr>
396	<tr>
397	<td><i>Name</i></td>
398	<td>\Probe Set ID\</td>
399	</tr>
400	<tr>
401	<td><i>External ID</i></td>
402	<td>\Probe Set ID\</td>
403	</tr>
404	<tr>
405	<td><i>Description</i></td>
406	<td>\Target Description\</td>
407	</tr>
408	<tr>
409	<td><i>Gene symbol</i></td>
410	<td>\Gene Symbol\</td>
411	</tr>
412	</table>
413
414	</td>
415	</tr>
416	</table>
417	<p>
418	</li>
419
420	<li>
421	Import reporters:
422	<ol>
423	<li>Go to the <code>View -> Reporters</code> page.</li>
424	<li>Click on the <code>Import</code> button.</li>
425	<li>Choose <code>auto-detect</code> and then upload
426	the file <code>plates_and_reporters.mouse.v4.37k.txt</code>.</li>
427	<li>The <code>Reporters for project A</code> format should be
428	found.</li>
429	<li>Select the <code>skip</code> option for the "Missing a required" value
430	since the file contains rows with empty reporter ID:s.
431	<li>Continue and wait for the import to finish. It should create 35,912 new reporters.</li>
432	<li>
433	Repeat the procedure with the <code>MG_U74Av2_annot.csv</code> file. This time
434	also select <code>crop</code> for the "String too long" setting since
435	the file contains data that is too large for the datbase.
436	12,488 new reporters should be created.
437	</ol>
438	<p>
439
440	</li>
441
442
443	</ol>
444
445
446	<a name="power"></a>
447	<h2>4. Power user tests</h2>
448	<p>
449	The power user is the typical owner/administrator of a project. The power user sets
450	up common resources used in the project, such as hardware, software, protocols,
451	file formats and annotation types. In this case the power user is also responsible for
452	managing the LIMS.
453	</p>
454
455	<ol>
456	<li>
457	Create a project:
458
459	<table class="listing" cellspacing="0" cellpadding="2" border="0">
460	<tr>
461	<th>Name</th>
462	<th>Members</th>
463	</tr>
464	<tr>
465	<td>Project A</td>
466	<td>Groups: Group A (Use permission)</td>
467	</tr>
468	</table>
469	<p>
470	</li>
471
472	<li>Activate the project.<p></li>
473
474	<li>
475	Create protocols:
476	<table class="listing" cellspacing="0" cellpadding="2" border="0">
477	<tr>
478	<th>Name</th>
479	<th>Type</th>
480	</tr>
481	<tr>
482	<td>Sampling A</td>
483	<td>Sampling</td>
484	</tr>
485	<tr>
486	<td>Extraction A</td>
487	<td>Extraction</td>
488	</tr>
489	<tr>
490	<td>Labeling A</td>
491	<td>Labeling</td>
492	</tr>
493	<tr>
494	<td>Hybridization A</td>
495	<td>Hybridization</td>
496	</tr>
497	<tr>
498	<td>Scanning A</td>
499	<td>Scanning</td>
500	</tr>
501	<tr>
502	<td>Feature extraction A</td>
503	<td>Feature extraction</td>
504	</tr>
505	<tr>
506	<td>Printing A</td>
507	<td>Printing</td>
508	</tr>
509	</table>
510	<p>
511	</li>
512
513	<li>
514	Create hardware:
515	<table class="listing" cellspacing="0" cellpadding="2" border="0">
516	<tr>
517	<th>Name</th>
518	<th>Type</th>
519	</tr>
520	<tr>
521	<td>Hybridization station A</td>
522	<td>Hybridization station</td>
523	</tr>
524	<tr>
525	<td>Scanner A</td>
526	<td>Scanner</td>
527	</tr>
528	<tr>
529	<td>Print robot A</td>
530	<td>Print robot</td>
531	</tr>
532	</table>
533	<p>
534	</li>
535
536	<li>
537	Create software:
538	<table class="listing" cellspacing="0" cellpadding="2" border="0">
539	<tr>
540	<th>Name</th>
541	<th>Type</th>
542	</tr>
543	<tr>
544	<td>Software A</td>
545	<td>Feature extraction</td>
546	</tr>
547	</table>
548	<p>
549	</li>
550
551	<li>
552	Create annotation types:
553	<table class="listing" cellspacing="0" cellpadding="2" border="0">
554	<tr>
555	<th>Name</th>
556	<th>Type</th>
557	<th>Unit</th>
558	<th>Interface</th>
559	<th>Values</th>
560	<th>Item types</th>
561	</tr>
562	<tr>
563	<td>Drug resistance</td>
564	<td>String</td>
565	<td>-</td>
566	<td>radiobuttons</td>
567	<td>high, medium, low</td>
568	<td>Biosource</td>
569	</tr>
570	<tr>
571	<td>Time</td>
572	<td>Integer</td>
573	<td>Hour</td>
574	<td>text box</td>
575	<td>-</td>
576	<td>Sample</td>
577	</tr>
578	<tr>
579	<td>Dye swap</td>
580	<td>Boolean</td>
581	<td>-</td>
582	<td>-</td>
583	<td>-</td>
584	<td>Raw bioassay</td>
585	</tr>
586	</table>
587	<p>
588
589	<li>
590	Create file formats (<i>i.e.</i>, plug-in configurations). The formats marked as
591	optional are not used in the test procedure, but may be useful to weed
592	out import problems, since they allow importing all info from the raw
593	data files. You may either enter the regular expressions as specified or
594	use the "Test with file" feature.
595
596	<table class="listing" cellspacing="0" cellpadding="2" border="0">
597	<tr>
598	<th>Name</th>
599	<th>Plugin</th>
600	<th>Configuration values</th>
601	</tr>
602
603	<tr class="oddrow">
604	<td>Plates for project A</td>
605	<td>Plate importer</td>
606	<td>
607
608	<b>Test with file:</b> <code>plates_and_reporters.mouse.v4.37k.txt</code>
609	<table border="0" cellspacing="0" cellpadding="2">
610	<tr>
611	<td><i>Data header</i></td>
612	<td>384_number\t384_column\t384_row\t384_position\toligo_id.*</td>
613	</tr>
614	<tr>
615	<td><i>Data splitter</i></td>
616	<td>\t</td>
617	</tr>
618	<tr>
619	<td><i>Min data columns</i></td>
620	<td>5</td>
621	</tr>
622	<tr>
623	<td><i>Plate number/name</i></td>
624	<td>\384_number\</td>
625	</tr>
626	<tr>
627	<td><i>Row</i></td>
628	<td>\384_row\</td>
629	</tr>
630	<tr>
631	<td><i>Column</i></td>
632	<td>\384_column\</td>
633	</tr>
634	<tr>
635	<td><i>Reporter ID</i></td>
636	<td>\oligo_id\</td>
637	</tr>
638	</table>
639
640	</td>
641	</tr>
642
643	<tr class="evenrow">
644	<td>GenePix feature importer<br>(optional)</td>
645	<td>Reporter map importer</td>
646	<td>
647
648	<b>Test with file:</b> <code>genepix.mouse.v4.37k.00h.gpr</code>
649	<table border="0" cellspacing="0" cellpadding="2">
650	<tr>
651	<td><i>Data header</i></td>
652	<td>"Block"\t"Column"\t"Row"\t"Name"\t"ID"\t.*</td>
653	</tr>
654	<tr>
655	<td><i>Data splitter</i></td>
656	<td>\t</td>
657	</tr>
658	<tr>
659	<td><i>Min data columns</i></td>
660	<td>48</td>
661	</tr>
662	<tr>
663	<td><i>Max data columns</i></td>
664	<td>48</td>
665	</tr>
666	<tr>
667	<td><i>Reporter ID</i></td>
668	<td>\ID\</td>
669	</tr>
670	<tr>
671	<td><i>Block</i></td>
672	<td>\Block\</td>
673	</tr>
674	<tr>
675	<td><i>Column</i></td>
676	<td>\Column\</td>
677	</tr>
678	<tr>
679	<td><i>Row</i></td>
680	<td>\Row\</td>
681	</tr>
682	</table>
683
684	</td>
685	</tr>
686
687	<tr class="oddrow">
688	<td>Raw data for project A</td>
689	<td>Raw data importer</td>
690	<td>
691
692	<b>Test with file:</b> <code>genepix.mouse.v4.37k.00h.gpr</code>
693	<table border="0" cellspacing="0" cellpadding="2">
694	<tr>
695	<td><i>Raw data type</i></td>
696	<td>Genepix</td>
697	</tr>
698	<tr>
699	<td><i>Header</i></td>
700	<td>"(.+)=(.*)"</td>
701	</tr>
702	<tr>
703	<td><i>Data header</i></td>
704	<td>"Block"\t"Column"\t"Row"\t"Name"\t"ID"\t."Ratio of Medians $532\/635$".</td>
705	</tr>
706	<tr>
707	<td><i>Data splitter</i></td>
708	<td>\t</td>
709	</tr>
710	<tr>
711	<td><i>Min data columns</i></td>
712	<td>48</td>
713	</tr>
714	<tr>
715	<td><i>Max data columns</i></td>
716	<td>48</td>
717	</tr>
718
719	<tr>
720	<td><i>Block</i></td>
721	<td>\Block\</td>
722	</tr>
723	<tr>
724	<td><i>Column</i></td>
725	<td>\Column\</td>
726	</tr>
727	<tr>
728	<td><i>Row</i></td>
729	<td>\Row\</td>
730	</tr>
731	<tr>
732	<td><i>X</i></td>
733	<td>\X\</td>
734	</tr>
735	<tr>
736	<td><i>Y</i></td>
737	<td>\Y\</td>
738	</tr>
739	<tr>
740	<td><i>Reporter ID</i></td>
741	<td>\ID\</td>
742	</tr>
743	<tr>
744	<td><i>Spot diameter</i></td>
745	<td>\Dia.\</td>
746	</tr>
747	<tr>
748	<td><i>Channel 1 foreground median</i></td>
749	<td>\F635 Median\</td>
750	</tr>
751	<tr>
752	<td><i>Channel 1 foreground mean</i></td>
753	<td>\F635 Mean\</td>
754	</tr>
755	<tr>
756	<td><i>Channel 1 foreground standard deviation</i></td>
757	<td>\F635 SD\</td>
758	</tr>
759	<tr>
760	<td><i>Channel 1 background median</i></td>
761	<td>\B635 Median\</td>
762	</tr>
763	<tr>
764	<td><i>Channel 1 background mean</i></td>
765	<td>\B635 Mean\</td>
766	</tr>
767	<tr>
768	<td><i>Channel 1 background standard deviation</i></td>
769	<td>\B635 SD\</td>
770	</tr>
771	<tr>
772	<td><i>Percent pixels within 1 standard deviation</i></td>
773	<td>\% > B635+1SD\</td>
774	</tr>
775	<tr>
776	<td><i>Percent pixels within 2 standard deviations</i></td>
777	<td>\% > B635+2SD\</td>
778	</tr>
779	<tr>
780	<td><i>Percent saturated pixels</i></td>
781	<td>\F635 % Sat.\</td>
782	</tr>
783	<tr>
784	<td><i>Channel 2 foreground median</i></td>
785	<td>\F532 Median\</td>
786	</tr>
787	<tr>
788	<td><i>Channel 2 foreground mean</i></td>
789	<td>\F532 Mean\</td>
790	</tr>
791	<tr>
792	<td><i>Channel 2 foreground standard deviation</i></td>
793	<td>\F532 SD\</td>
794	</tr>
795	<tr>
796	<td><i>Channel 2 background median</i></td>
797	<td>\B532 Median\</td>
798	</tr>
799	<tr>
800	<td><i>Channel 2 background mean</i></td>
801	<td>\B532 Mean\</td>
802	</tr>
803	<tr>
804	<td><i>Channel 2 background standard deviation</i></td>
805	<td>\B532 SD\</td>
806	</tr>
807	<tr>
808	<td><i>Percent pixels within 1 standard deviation</i></td>
809	<td>\% > B532+1SD\</td>
810	</tr>
811	<tr>
812	<td><i>Percent pixels within 2 standard deviations</i></td>
813	<td>\% > B532+2SD\</td>
814	</tr>
815	<tr>
816	<td><i>Percent saturated pixels</i></td>
817	<td>\F532 % Sat.\</td>
818	</tr>
819	<tr>
820	<td><i>Foreground pixels</i></td>
821	<td>\F Pixels\</td>
822	</tr>
823	<tr>
824	<td><i>Background pixels</i></td>
825	<td>\B Pixels\</td>
826	</tr>
827	<tr>
828	<td><i>Flags</i></td>
829	<td>\Flags\</td>
830	</tr>
831	</table>
832
833	</td>
834	</tr>
835
836	<tr class="evenrow">
837	<td>Raw data for project A (dye-swap)</td>
838	<td>Raw data importer</td>
839	<td>
840
841	<b>Test with file:</b> <code>genepix.mouse.v4.37k.00h.dyeswap.gpr</code>
842	<table border="0" cellspacing="0" cellpadding="2">
843	<tr>
844	<td><i>Raw data type</i></td>
845	<td>Genepix</td>
846	</tr>
847	<tr>
848	<td><i>Header</i></td>
849	<td>"(.+)=(.*)"</td>
850	</tr>
851	<tr>
852	<td><i>Data header</i></td>
853	<td>"Block"\t"Column"\t"Row"\t"Name"\t"ID"\t."Ratio of Medians $635\/532$".</td>
854	</tr>
855	<tr>
856	<td><i>Data splitter</i></td>
857	<td>\t</td>
858	</tr>
859	<tr>
860	<td><i>Min data columns</i></td>
861	<td>48</td>
862	</tr>
863	<tr>
864	<td><i>Max data columns</i></td>
865	<td>48</td>
866	</tr>
867
868	<tr>
869	<td><i>Block</i></td>
870	<td>\Block\</td>
871	</tr>
872	<tr>
873	<td><i>Column</i></td>
874	<td>\Column\</td>
875	</tr>
876	<tr>
877	<td><i>Row</i></td>
878	<td>\Row\</td>
879	</tr>
880	<tr>
881	<td><i>X</i></td>
882	<td>\X\</td>
883	</tr>
884	<tr>
885	<td><i>Y</i></td>
886	<td>\Y\</td>
887	</tr>
888	<tr>
889	<td><i>Reporter ID</i></td>
890	<td>\ID\</td>
891	</tr>
892	<tr>
893	<td><i>Spot diameter</i></td>
894	<td>\Dia.\</td>
895	</tr>
896	<tr>
897	<td><i>Channel 1 foreground median</i></td>
898	<td>\F532 Median\</td>
899	</tr>
900	<tr>
901	<td><i>Channel 1 foreground mean</i></td>
902	<td>\F532 Mean\</td>
903	</tr>
904	<tr>
905	<td><i>Channel 1 foreground standard deviation</i></td>
906	<td>\F532 SD\</td>
907	</tr>
908	<tr>
909	<td><i>Channel 1 background median</i></td>
910	<td>\B532 Median\</td>
911	</tr>
912	<tr>
913	<td><i>Channel 1 background mean</i></td>
914	<td>\B532 Mean\</td>
915	</tr>
916	<tr>
917	<td><i>Channel 1 background standard deviation</i></td>
918	<td>\B532 SD\</td>
919	</tr>
920	<tr>
921	<td><i>Percent pixels within 1 standard deviation</i></td>
922	<td>\% > B532+1SD\</td>
923	</tr>
924	<tr>
925	<td><i>Percent pixels within 2 standard deviations</i></td>
926	<td>\% > B532+2SD\</td>
927	</tr>
928	<tr>
929	<td><i>Percent saturated pixels</i></td>
930	<td>\F532 % Sat.\</td>
931	</tr>
932	<tr>
933	<td><i>Channel 2 foreground median</i></td>
934	<td>\F635 Median\</td>
935	</tr>
936	<tr>
937	<td><i>Channel 2 foreground mean</i></td>
938	<td>\F635 Mean\</td>
939	</tr>
940	<tr>
941	<td><i>Channel 2 foreground standard deviation</i></td>
942	<td>\F635 SD\</td>
943	</tr>
944	<tr>
945	<td><i>Channel 2 background median</i></td>
946	<td>\B635 Median\</td>
947	</tr>
948	<tr>
949	<td><i>Channel 2 background mean</i></td>
950	<td>\B635 Mean\</td>
951	</tr>
952	<tr>
953	<td><i>Channel 2 background standard deviation</i></td>
954	<td>\B635 SD\</td>
955	</tr>
956	<tr>
957	<td><i>Percent pixels within 1 standard deviation</i></td>
958	<td>\% > B635+1SD\</td>
959	</tr>
960	<tr>
961	<td><i>Percent pixels within 2 standard deviations</i></td>
962	<td>\% > B635+2SD\</td>
963	</tr>
964	<tr>
965	<td><i>Percent saturated pixels</i></td>
966	<td>\F635 % Sat.\</td>
967	</tr>
968	<tr>
969	<td><i>Foreground pixels</i></td>
970	<td>\F Pixels\</td>
971	</tr>
972	<tr>
973	<td><i>Background pixels</i></td>
974	<td>\B Pixels\</td>
975	</tr>
976	<tr>
977	<td><i>Flags</i></td>
978	<td>\Flags\</td>
979	</tr>
980	</table>
981
982	</td>
983	</tr>
984	</table>
985	<p>
986	</li>
987
988	<li>
989	Annotate the file formats:
990	<table class="listing" cellspacing="0" cellpadding="2" border="0">
991	<tr>
992	<th>File format</th>
993	<th>Annotation</th>
994	<th>Value</th>
995	</tr>
996	<tr>
997	<td>Raw data for project A</td>
998	<td>Dye swap</td>
999	<td>false</td>
1000	</tr>
1001	<tr>
1002	<td>Raw data for project A (dye swap)</td>
1003	<td>Dye swap</td>
1004	<td>true</td>
1005	</tr>
1006	</table>
1007	This will make the raw data importer automatically annotate the
1008	raw bioassays with the specified annotations.
1009	<p>
1010	</li>
1011
1012	<li>
1013	Create plate type:
1014	<table class="listing" cellspacing="0" cellpadding="2" border="0">
1015	<tr>
1016	<th>Name</th>
1017	<th>Geometry</th>
1018	</tr>
1019	<tr>
1020	<td>Plate type A</td>
1021	<td>384-well (16 x 24)</td>
1022	</tr>
1023	</table>
1024	<p>
1025	</li>
1026
1027	<li>
1028	Import plates:
1029	<ol>
1030	<li>Go to the <code>Array LIMS -> Plates</code> page.</li>
1031	<li>Click on the <code>Import</code> button.</li>
1032	<li>Choose <code>auto-detect</code> and select
1033	the file <code>plates_and_reporters.mouse.v4.37k.txt</code>.</li>
1034	<li>The <code>Plates for project A</code> format should be
1035	found.</li>
1036	<li>Specify the following parameters:
1037
1038	<table border="0" cellspacing="0" cellpadding="2">
1039	<tr>
1040	<td><i>Plate type</i></td>
1041	<td>Plate type A</td>
1042	</tr>
1043	<tr>
1044	<td><i>Plate name prefix</i></td>
1045	<td>Plate A</td>
1046	</tr>
1047	<tr>
1048	<td><i>Plate name padding</i></td>
1049	<td>4</td>
1050	</tr>
1051	</table>
1052	</li>
1053	<li>Continue and wait for the import to finish. It should create 96 plates.</li>
1054	</ol>
1055	<p>
1056	</li>
1057
1058	<li>
1059	Create array designs and upload data files to them:
1060	<table class="listing" cellspacing="0" cellpadding="2" border="0">
1061	<tr>
1062	<th>Name</th>
1063	<th>Platform</th>
1064	<th>File(s)</th>
1065	</tr>
1066	<tr>
1067	<td>Array design A</td>
1068	<td>Generic</td>
1069	<td><i>Print map</i>: printmap.mouse.v4.37k.tam</td>
1070	</tr>
1071	<tr>
1072	<td>Affymetrix A</td>
1073	<td>Affymetrix</td>
1074	<td><i>CDF file</i>: MG_U74Av2.cdf.bz2</td>
1075	</tr>
1076	</table>
1077	<p>
1078	</li>
1079
1080	<li>
1081	Connect <code>Array design A</code> with plates. Select the imported plates (plate names starting
1082	with <code>Plate A</code>) and sort them in the correct order (as indicated by their names).
1083	<p>
1084	</li>
1085
1086	<li>
1087	Import features:
1088	<ol>
1089	<li>Click on the <code>Import</code> button when viewing properties for the array design.</li>
1090	<li>Choose <code>auto-detect</code> and upload the file
1091	<code>printmap.mouse.v4.37k.tam</code>.</li>
1092	<li>The <code>Print map importer</code> plug-in should be
1093	found.</li>
1094	<li>Continue and wait for the import to finish. It should create 36,864 features and 48 blocks.</li>
1095	</ol>
1096	<p>
1097	</li>
1098
1099	<li>
1100	Set project defaults. Go to the projects page and edit the
1101	<code>Project A</code> project. On the <code>Defaults</code>
1102	tab, set the following defaults:
1103
1104	<table class="listing" cellspacing="0" cellpadding="2" border="0">
1105	<tr>
1106	<th>Setting</th>
1107	<th>Value</th>
1108	</tr>
1109	<tr>
1110	<td>Platform / raw data type</td>
1111	<td>Generic / Genepix</td>
1112	</tr>
1113	<tr>
1114	<td>Software</td>
1115	<td>Software A</td>
1116	</tr>
1117	<tr>
1118	<td>Array design</td>
1119	<td>Array design A</td>
1120	</tr>
1121	<tr>
1122	<td>Hybridization station</td>
1123	<td>Hybridization station A</td>
1124	</tr>
1125	<tr>
1126	<td>Scanner</td>
1127	<td>Scanner A</td>
1128	</tr>
1129	<tr>
1130	<td>Print robot</td>
1131	<td>Print robot A</td>
1132	</tr>
1133	<tr>
1134	<td>Scanning protocol</td>
1135	<td>Scanning A</td>
1136	</tr>
1137	<tr>
1138	<td>Sampling protocol</td>
1139	<td>Sampling A</td>
1140	</tr>
1141	<tr>
1142	<td>Extraction protocol</td>
1143	<td>Extraction A</td>
1144	</tr>
1145	<tr>
1146	<td>Labeling protocol</td>
1147	<td>Labeling A</td>
1148	</tr>
1149	<tr>
1150	<td>Hybridization protocol</td>
1151	<td>Hybridization A</td>
1152	</tr>
1153	<tr>
1154	<td>Feat. extraction protocol</td>
1155	<td>Feature extraction A</td>
1156	</tr>
1157	<tr>
1158	<td>Printing protocol</td>
1159	<td>Printing A</td>
1160	</tr>
1161	</table>
1162
1163	<p>
1164	</li>
1165
1166	<li>
1167	Create array batches:
1168	<table class="listing" cellspacing="0" cellpadding="2" border="0">
1169	<tr>
1170	<th>Name</th>
1171	<th>Array design</th>
1172	<th>Print robot</th>
1173	<th>Protocol</th>
1174	</tr>
1175	<tr>
1176	<td>Array batch A</td>
1177	<td>Array design A</td>
1178	<td>Robot A</td>
1179	<td>Printing A</td>
1180	</tr>
1181	<tr>
1182	<td>Affymetrix batch A</td>
1183	<td>Affymetrix A</td>
1184	<td></td>
1185	<td></td>
1186	</tr>
1187	</table>
1188	<p>
1189	</li>
1190
1191	<li>
1192	Create array slides with the <code>Create slides</code>
1193	wizard.
1194
1195	<table class="listing" cellspacing="0" cellpadding="2" border="0">
1196	<tr>
1197	<th>Name</th>
1198	<th>Array batch</th>
1199	<th>Quantity</th>
1200	</tr>
1201	<tr>
1202	<td>Array slide A.</td>
1203	<td>Array batch A</td>
1204	<td>4</td>
1205	</tr>
1206	<tr>
1207	<td>Affymetrix slide A.</td>
1208	<td>Affymetrix batch A</td>
1209	<td>3</td>
1210	</tr>
1211	</table>
1212	<p>
1213	</li>
1214	</ol>
1215
1216	<a name="user"></a>
1217	<h2>5. User tests</h2>
1218	<p>
1219	The user is a typical worker in the project. The user does the actual experimentation in the
1220	lab, which includes collecting samples, doing extraction, labeling and hybridizations.
1221	The user also scans and analyses the raw data resulting from the images.
1222	</p>
1223
1224	<ol>
1225	<li>
1226	Activate the <code>Project A</code> project<p></li>
1227
1228	<li>
1229	Create a biosource:
1230	<table class="listing" cellspacing="0" cellpadding="2" border="0">
1231	<tr>
1232	<th>Name</th>
1233	<th>Annotations</th>
1234	</tr>
1235	<tr>
1236	<td>Biosource A</td>
1237	<td>
1238	<table border="0" cellspacing="0" cellpadding="2">
1239	<tr>
1240	<td><i>Drug resistance:</i></td>
1241	<td>medium</td>
1242	</tr>
1243	</table>
1244	</td>
1245	</tr>
1246	</table>
1247	<p>
1248	</li>
1249
1250	<li>
1251	Create samples:
1252	<table class="listing" cellspacing="0" cellpadding="2" border="0">
1253	<tr>
1254	<th>Name</th>
1255	<th>Protocol</th>
1256	<th>Biosource</th>
1257	<th>Annotations</th>
1258	</tr>
1259	<tr>
1260	<td>Sample A.00h</td>
1261	<td>Sampling A</td>
1262	<td>Biosource A</td>
1263	<td>
1264	<table border="0" cellspacing="0" cellpadding="2">
1265	<tr>
1266	<td><i>Time (hours):</i></td>
1267	<td>0</td>
1268	</tr>
1269	</table>
1270	</td>
1271	</tr>
1272	<tr>
1273	<td>Sample A.24h</td>
1274	<td>Sampling A</td>
1275	<td>Biosource A</td>
1276	<td>
1277	<table border="0" cellspacing="0" cellpadding="2">
1278	<tr>
1279	<td><i>Time (hours):</i></td>
1280	<td>24</td>
1281	</tr>
1282	</table>
1283	</td>
1284	</tr>
1285	<tr>
1286	<td>Sample A.ref</td>
1287	<td>Sampling A</td>
1288	<td>-</td>
1289	<td>-</td>
1290	</tr>
1291	</table>
1292	<p>
1293	</li>
1294
1295	<li>
1296	Create extracts:
1297	<table class="listing" cellspacing="0" cellpadding="2" border="0">
1298	<tr>
1299	<th>Name</th>
1300	<th>Protocol</th>
1301	<th>Sample</th>
1302	</tr>
1303	<tr>
1304	<td>Extract A.00h</td>
1305	<td>Extraction A</td>
1306	<td>Sample A.00h</td>
1307	</tr>
1308	<tr>
1309	<td>Extract A.24h</td>
1310	<td>Extraction A</td>
1311	<td>Sample A.24h</td>
1312	</tr>
1313	<tr>
1314	<td>Extract A.ref</td>
1315	<td>Extraction A</td>
1316	<td>Sample A.ref</td>
1317	</tr>
1318	</table>
1319	<p>
1320	</li>
1321
1322	<li>
1323	Create labeled extracts:
1324	<table class="listing" cellspacing="0" cellpadding="2" border="0">
1325	<tr>
1326	<th>Name</th>
1327	<th>Label</th>
1328	<th>Protocol</th>
1329	<th>Extract</th>
1330	</tr>
1331	<tr>
1332	<td>Labeled extract A.00h</td>
1333	<td>cy3</td>
1334	<td>Labeling A</td>
1335	<td>Extract A.00h</td>
1336	</tr>
1337	<tr>
1338	<td>Labeled extract A.24h</td>
1339	<td>cy3</td>
1340	<td>Labeling A</td>
1341	<td>Extract A.24h</td>
1342	</tr>
1343	<tr>
1344	<td>Labeled extract A.ref</td>
1345	<td>cy5</td>
1346	<td>Labeling A</td>
1347	<td>Extract A.ref</td>
1348	</tr>
1349	<tr class="shaded">
1350	<td>Labeled extract A.00h (dye-swap)</td>
1351	<td>cy5</td>
1352	<td>Labeling A</td>
1353	<td>Extract A.00h</td>
1354	</tr>
1355	<tr class="shaded">
1356	<td>Labeled extract A.24h (dye-swap)</td>
1357	<td>cy5</td>
1358	<td>Labeling A</td>
1359	<td>Extract A.24h</td>
1360	</tr>
1361	<tr class="shaded">
1362	<td>Labeled extract A.ref (dye-swap)</td>
1363	<td>cy3</td>
1364	<td>Labeling A</td>
1365	<td>Extract A.ref</td>
1366	</tr>
1367	</table>
1368	<p>
1369	</li>
1370
1371	<li>
1372	Create hybridizations:
1373	<table class="listing" cellspacing="0" cellpadding="2" border="0">
1374	<tr>
1375	<th>Name</th>
1376	<th>Protocol</th>
1377	<th>Hardware</th>
1378	<th>Array slide</th>
1379	<th>Labeled extracts</th>
1380	</tr>
1381	<tr>
1382	<td>Hybridization A.00h</td>
1383	<td>Hybridization A</td>
1384	<td>Hybridization station A</td>
1385	<td>Array slide A.1</td>
1386	<td>Labeled extract A.00h,<br>Labeled extract A.ref</td>
1387	</tr>
1388	<tr>
1389	<td>Hybridization A.24h</td>
1390	<td>Hybridization A</td>
1391	<td>Hybridization station A</td>
1392	<td>Array slide A.2</td>
1393	<td>Labeled extract A.24h,<br>Labeled extract A.ref</td>
1394	</tr>
1395	<tr class="shaded">
1396	<td>Hybridization A.00h (dye-swap)</td>
1397	<td>Hybridization A</td>
1398	<td>Hybridization station A</td>
1399	<td>Array slide A.3</td>
1400	<td>Labeled extract A.00h (dye-swap),<br>Labeled extract A.ref (dye-swap)</td>
1401	</tr>
1402	<tr class="shaded">
1403	<td>Hybridization A.24h (dye-swap)</td>
1404	<td>Hybridization A</td>
1405	<td>Hybridization station A</td>
1406	<td>Array slide A.4</td>
1407	<td>Labeled extract A.24h (dye-swap),<br>Labeled extract A.ref (dye-swap)</td>
1408	</tr>
1409	<tr>
1410	<td>Affymetrix hyb A.1</td>
1411	<td>Hybridization A</td>
1412	<td>Hybridization station A</td>
1413	<td>Affymetrix slide A.1</td>
1414	<td>Labeled extract A.00h</td>
1415	</tr>
1416	<tr>
1417	<td>Affymetrix hyb A.2</td>
1418	<td>Hybridization A</td>
1419	<td>Hybridization station A</td>
1420	<td>Affymetrix slide A.2</td>
1421	<td>Labeled extract A.24h</td>
1422	</tr>
1423	<tr>
1424	<td>Affymetrix hyb A.3</td>
1425	<td>Hybridization A</td>
1426	<td>Hybridization station A</td>
1427	<td>Affymetrix slide A.3</td>
1428	<td>Labeled extract A.ref</td>
1429	</tr>
1430	</table>
1431	<p>
1432	</li>
1433
1434	<li>
1435	Create scans:
1436	<table class="listing" cellspacing="0" cellpadding="2" border="0">
1437	<tr>
1438	<th>Name</th>
1439	<th>Hybridization</th>
1440	<th>Scanner</th>
1441	<th>Protocol</th>
1442	</tr>
1443	<tr>
1444	<td>Scan A.00h</td>
1445	<td>Hybridization A.00h</td>
1446	<td>Scanner A</td>
1447	<td>Scanning A</td>
1448	</tr>
1449	<tr>
1450	<td>Scan A.24h</td>
1451	<td>Hybridization A.24h</td>
1452	<td>Scanner A</td>
1453	<td>Scanning A</td>
1454	</tr>
1455	<tr class="shaded">
1456	<td>Scan A.00h (dye-swap)</td>
1457	<td>Hybridization A.00h (dye-swap)</td>
1458	<td>Scanner A</td>
1459	<td>Scanning A</td>
1460	</tr>
1461	<tr class="shaded">
1462	<td>Scan A.24h (dye-swap)</td>
1463	<td>Hybridization A.24h (dye-swap)</td>
1464	<td>Scanner A</td>
1465	<td>Scanning A</td>
1466	</tr>
1467	<tr>
1468	<td>Affymetrix scan A.1</td>
1469	<td>Affymetrix hyb A.1</td>
1470	<td>Scanner A</td>
1471	<td>Scanning A</td>
1472	</tr>
1473	<tr>
1474	<td>Affymetrix scan A.2</td>
1475	<td>Affymetrix hyb A.2</td>
1476	<td>Scanner A</td>
1477	<td>Scanning A</td>
1478	</tr>
1479	<tr>
1480	<td>Affymetrix scan A.3</td>
1481	<td>Affymetrix hyb A.3</td>
1482	<td>Scanner A</td>
1483	<td>Scanning A</td>
1484	</tr>
1485	</table>
1486	<p>
1487	</li>
1488
1489	<li>
1490	Add images to the scans (TODO - we don't have any images yet):
1491	<table class="listing" cellspacing="0" cellpadding="2" border="0">
1492	<tr>
1493	<th>Scan</th>
1494	<th>Image files</th>
1495	</tr>
1496	<tr>
1497	<td>Scan A.00h</td>
1498	<td>-</td>
1499	</tr>
1500	<tr>
1501	<td>Scan A.24h</td>
1502	<td>-</td>
1503	</tr>
1504	<tr class="shaded">
1505	<td>Scan A.00h (dye-swap)</td>
1506	<td>-</td>
1507	</tr>
1508	<tr class="shaded">
1509	<td>Scan A.24h (dye-swap)</td>
1510	<td>-</td>
1511	</tr>
1512	</table>
1513	<p>
1514	</li>
1515
1516	<li>
1517	Create raw bioassays:
1518	<table class="listing" cellspacing="0" cellpadding="2" border="0">
1519	<tr>
1520	<th>Name</th>
1521	<th>Platform/Raw data type</th>
1522	<th>Array design</th>
1523	<th>Protocol</th>
1524	<th>Scan</th>
1525	<th>Software</th>
1526	<th>File(s)</th>
1527	</tr>
1528	<tr>
1529	<td>Raw bioassay A.00h</td>
1530	<td>Generic/GenePix</td>
1531	<td>Array design A</td>
1532	<td>Feature extraction A</td>
1533	<td>Scan A.00h</td>
1534	<td>Software A</td>
1535	<td><i>Raw data</i>: genepix.mouse.v4.37k.00h.gpr</td>
1536	</tr>
1537	<tr>
1538	<td>Raw bioassay A.24h</td>
1539	<td>Generic/GenePix</td>
1540	<td>Array design A</td>
1541	<td>Feature extraction A</td>
1542	<td>Scan A.24h</td>
1543	<td>Software A</td>
1544	<td><i>Raw data</i>: genepix.mouse.v4.37k.24h.gpr</td>
1545	</tr>
1546	<tr class="shaded">
1547	<td>Raw bioassay A.00h (dye-swap)</td>
1548	<td>Generic/GenePix</td>
1549	<td>Array design A</td>
1550	<td>Feature extraction A</td>
1551	<td>Scan A.00h (dye-swap)</td>
1552	<td>Software A</td>
1553	<td><i>Raw data</i>: genepix.mouse.v4.37k.00h.dyeswap.gpr</td>
1554	</tr>
1555	<tr class="shaded">
1556	<td>Raw bioassay A.24h (dye-swap)</td>
1557	<td>Generic/GenePix</td>
1558	<td>Array design A</td>
1559	<td>Feature extraction A</td>
1560	<td>Scan A.24h (dye-swap)</td>
1561	<td>Software A</td>
1562	<td><i>Raw data</i>: genepix.mouse.v4.37k.24h.dyeswap.gpr</td>
1563	</tr>
1564	<tr>
1565	<td>Affymetrix raw A.1</td>
1566	<td>Affymetrix</td>
1567	<td>Affymetrix A</td>
1568	<td>Feature extraction A</td>
1569	<td>Affymetrix scan A.1</td>
1570	<td>Software A</td>
1571	<td><i>CEL file</i>: jos1761.cel.bz2</td>
1572	</tr>
1573	<tr>
1574	<td>Affymetrix raw A.2</td>
1575	<td>Affymetrix</td>
1576	<td>Affymetrix A</td>
1577	<td>Feature extraction A</td>
1578	<td>Affymetrix scan A.2</td>
1579	<td>Software A</td>
1580	<td><i>CEL file</i>: jos1762.cel.bz2</td>
1581	</tr>
1582	<tr>
1583	<td>Affymetrix raw A.3</td>
1584	<td>Affymetrix</td>
1585	<td>Affymetrix A</td>
1586	<td>Feature extraction A</td>
1587	<td>Affymetrix scan A.3</td>
1588	<td>Software A</td>
1589	<td><i>CEL file</i>: jos1763.cel.bz2</td>
1590	</tr>
1591	</table>
1592	<p>
1593	</li>
1594
1595	<li>
1596	Inherit the annotations from the samples and biosource for each raw bioassay.
1597	<p>
1598
1599	</li>
1600
1601	<li>
1602	Use the auto-detect feature to upload and import raw data for each
1603	Genepix raw bioassay. Select the <code>smart</code> option for the "Feature mismatch"
1604	parameter and <code>null</code> for "Invalid numeric value".
1605
1606	<table class="listing" cellspacing="0" cellpadding="2" border="0">
1607	<tr>
1608	<th>Raw bioassay</th>
1609	<th>Raw data file</th>
1610	<th>Spots inserted/with null reporter/skipped)</th>
1611	<th>Annotations created</th>
1612	</tr>
1613	<tr>
1614	<td>Raw bioassay A.00h</td>
1615	<td>genepix.mouse.v4.37k.00h.gpr</td>
1616	<td>36,864/632/768</td>
1617	<td><i>Dye swap</i>: false</td>
1618	</tr>
1619	<tr>
1620	<td>Raw bioassay A.24h</td>
1621	<td>genepix.mouse.v4.37k.24h.gpr</td>
1622	<td>36,864/632/768</td>
1623	<td><i>Dye swap</i>: false</td>
1624	</tr>
1625	<tr class="shaded">
1626	<td>Raw bioassay A.00h (dye-swap)</td>
1627	<td>genepix.mouse.v4.37k.00h.dyeswap.gpr</td>
1628	<td>36,864/632/768</td>
1629	<td><i>Dye swap</i>: true</td>
1630	</tr>
1631	<tr class="shaded">
1632	<td>Raw bioassay A.24h (dye-swap)</td>
1633	<td>genepix.mouse.v4.37k.24h.dyeswap.gpr</td>
1634	<td>36,864/632/768</td>
1635	<td><i>Dye swap</i>: true</td>
1636	</tr>
1637	</table>
1638	<p>
1639	</li>
1640
1641	<li>
1642	Create experiments:
1643	<table class="listing" cellspacing="0" cellpadding="2" border="0">
1644	<tr>
1645	<th>Name</th>
1646	<th>Raw data type</th>
1647	<th>Raw bioassays</th>
1648	<th>Experimental factors</th>
1649	</tr>
1650	<tr>
1651	<td>Experiment A</td>
1652	<td>GenePix</td>
1653	<td>Raw bioassay A.00h,<br>Raw bioassay A.24h,<br>Raw bioassay A.00h (dye-swap),<br>
1654	Raw bioassay A.24h (dye-swap)</td>
1655	<td>Drug resistance, Time (hours), Dye swap</td>
1656	</tr>
1657	<tr>
1658	<td>Affymetrix A</td>
1659	<td>Affymetrix</td>
1660	<td>Affymetrix raw A.1,<br>Affymetrix raw A.2,<br>Affymetrix raw A.3</td>
1661	<td>Drug resistance, Time (hours)</td>
1662	</tr>
1663	</table>
1664	<p>
1665	</li>
1666
1667	<li>
1668	Check the experiment overview page. It should display one warnings for the
1669	Genepix experiment. The warning is related to a missing biosurce
1670	on the reference sample.
1671	<p>
1672	The Affymetrix experiment gives some more warnings. Most of them are
1673	related to not using the project default items, missing protocols
1674	and missing hardware. There should also be an error about missing
1675	experimental factor values for the <code>Affymetrix.3</code>
1676	raw bioassay. It is expected since this comes from the reference sample
1677	which doesn't have values for those annotations.
1678	<p>
1679
1680	Change validation options to reduce the number of warnings:
1681	<table class="listing" cellspacing="0" cellpadding="2" border="0">
1682	<tr>
1683	<th>Validation option</th>
1684	<th>Setting</th>
1685	</tr>
1686	<tr>
1687	<td>Project defaults</td>
1688	<td>Set all to <code>Ignore</code></td>
1689	</tr>
1690	<tr>
1691	<td>Missing items</td>
1692	<td>Set all to <code>Ignore</code></td>
1693	</tr>
1694	<tr>
1695	<td>Annotations - Missing factor value</td>
1696	<td><code>Warning</code></td>
1697	</tr>
1698	</table>
1699
1700	After the changes there should now only be two warnings about the
1701	missing factor values.
1702
1703	<p>
1704	</li>
1705
1706	</ol>
1707
1708	<a name="analysis"></a>
1709	<h2>6. Analysis tests</h2>
1710	<p>
1711	Now it is time to analyse the data. The analysis test should be done
1712	by both a regular user and a guest.
1713	</p>
1714
1715	<ol>
1716	<li>
1717	Activate the <code>Project A</code> project<p>
1718	</li>
1719
1720	<li>
1721	Go to the <code>Experiment A</code> experiment and select
1722	the <code>Bioassay sets</code> tab.
1723	<p>
1724	</li>
1725
1726	<li>
1727	Create a new root bioassay set:
1728	<table class="listing" cellspacing="0" cellpadding="2" border="0">
1729	<tr>
1730	<th>Bioassay set name</th>
1731	<th>Raw bioassays</th>
1732	<th>Formula</th>
1733	</tr>
1734	<tr>
1735	<td>Root bioassay set</td>
1736	<td>all</td>
1737	<td>Mean FG - Mean BG</td>
1738	</tr>
1739	</table>
1740	Wait for the plug-in to finish.
1741	<p>
1742	</li>
1743
1744	<li>
1745	Select the created bioassay set and create a filtered bioassayset:
1746	<table class="listing" cellspacing="0" cellpadding="2" border="0">
1747	<tr>
1748	<th>Child name</th>
1749	<th>Filter preset</th>
1750	<th>Expression</th>
1751	</tr>
1752	<tr>
1753	<td>Filtered bioassay set</td>
1754	<td>-</td>
1755	<td>ch(1) > 0 && ch(2) > 0 && rep('id') != null</td>
1756	</tr>
1757	</table>
1758	Wait for the plug-in to finish. It should report that 136,498 spots remain and
1759	that 10,958 spots has been removed.
1760	<p>
1761	</li>
1762
1763	<li>
1764	Select the filtered bioassay set and run a normalization plug-in:
1765	<table class="listing" cellspacing="0" cellpadding="2" border="0">
1766	<tr>
1767	<th>Plugin</th>
1768	<th>Parameters</th>
1769	</tr>
1770	<tr>
1771	<td>Normalization: Lowess</td>
1772	<td>Accept the most of default parameters, but change the
1773	"Block group size" to 12. Otherwise it will take too long time.</td>
1774	</tr>
1775	</table>
1776	Wait for the plug in to finish. It should report that 136,498 spots has been
1777	normalized and 0 spots has been removed.
1778	<p>
1779	</li>
1780
1781	<li>
1782	Select the normalized bioassay set and check the overview plots and
1783	the correction factor plots. Here are four examples:
1784	<table class="listing" cellspacing="0" cellpadding="2" border="0">
1785	<tr>
1786	<th>Overview plots</th>
1787	<th>Correction factor plots</th>
1788	</tr>
1789	<tr>
1790	<td><img src="overview.png"><br><img src="overview.dyeswap.png"></td>
1791	<td><img src="correction.png"><br><img src="correction.dyeswap.png"></td>
1792	</tr>
1793	</table>
1794	<p>
1795	</li>
1796
1797	<li>
1798	Try the plot tool with the following plots. Use the <code>Save</code> function
1799	to save one them as a file in the BASE file system, and the <code>Download</code>
1800	function to download a plot to your computer.
1801	<table class="listing" cellspacing="0" cellpadding="2" border="0">
1802	<tr>
1803	<th>Plot type</th>
1804	<th>Y-axis preset</th>
1805	<th>X-axis preset</th>
1806	<th>Other options</th>
1807	</tr>
1808	<tr>
1809	<td>Scatter plot</td>
1810	<td>M, log2(ch1 / ch2)</td>
1811	<td>A, log10(ch1 * ch2) / 2</td>
1812	<td>-</td>
1813	</tr>
1814	<tr>
1815	<td>Histogram plot</td>
1816	<td>Count</td>
1817	<td>Ratio, ch1 / ch2</td>
1818	<td>
1819	<table border="0" cellspacing="0" cellpadding="2">
1820	<tr>
1821	<td><i>Log scale</i></td>
1822	<td>checked</td>
1823	</tr>
1824	<tr>
1825	<td><i>Bin size</i></td>
1826	<td>0.1</td>
1827	</tr>
1828	<tr>
1829	<td><i>Annotation</i></td>
1830	<td>Time (hours)</td>
1831	</tr>
1832	</table>
1833	</td>
1834	</tr>
1835	</table>
1836	<p>
1837	Here are two examples:
1838	<table class="listing" cellspacing="0" cellpadding="2" border="0">
1839	<tr>
1840	<th>Scatter plot</th>
1841	</tr>
1842	<tr>
1843	<td><img src="scatter.png"></td>
1844	</tr>
1845	</table>
1846	<p>
1847	<table class="listing" cellspacing="0" cellpadding="2" border="0">
1848	<tr>
1849	<th>Histogram plot</th>
1850	</tr>
1851	<tr>
1852	<td><img src="histogram.png"></td>
1853	</tr>
1854	</table>
1855	<p>
1856	</li>
1857
1858	</ol>
1859
1860
1861	</body>
1862	</html>

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