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3	$Id: index.html 6124 2012-09-13 08:57:57Z nicklas $
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5	Copyright (C) 2006 Jari Häkkinen, Nicklas Nordborg, Martin Svensson
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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: 2012-09-13 08:57:57 +0000 (Thu, 13 Sep 2012) $
79	</p>
80	</div>
81
82
83	<a name="summary"></a>
84	<h2>1. Summary of the test procedure</h2>
85
86	<p>
87	Here is a summary of the test procedure:
88	</p>
89
90	<ol>
91	<li>Always start with a fresh installation.</li>
92
93	<li>The root user creates an administrator.</li>
94
95	<li>The administrator creates more users and some global resources:
96	<ul>
97	<li>A group and three other users. One power user, one user and one guest.</li>
98	<li>File formats for importing reporters</li>
99	<li>Imports reporters</li>
100	</ul>
101	</li>
102
103	<li>The power user creates item related to the project management:
104	<ul>
105	<li>A project</li>
106	<li>Protocols, one for each type of action: sampling, extraction, etc.</li>
107	<li>Hardware and software that are used in the project</li>
108	<li>Annotation types for annotations used in the project</li>
109	<li>File formats for importing plates, print maps and raw data</li>
110	<li>Array LIMS information - plate type, plates, array design, array batch and array slides</li>
111	<li>Biomaterial LIMS information - bioplate type</li>
112	</ul>
113	</li>
114
115	<li>The user creates items related to an actual experiment:
116	<ul>
117	<li>Biomaterials: bioplate, biosources, samples, extracts, etc.</li>
118	<li>Experiment: physical bioassays, derived bioassays, raw bioassays</li>
119	<li>Import raw data</li>
120	</ul>
121	</li>
122
123	<li>Both the user and the guest then do some analysis:
124	<ul>
125	<li>Create a root bioassay set</li>
126	<li>Filter the bioassay set</li>
127	<li>Run a normalization plug-in</li>
128	<li>Check the result by listing and plotting the data</li>
129	</ul>
130	</li>
131	</ol>
132
133	<p>
134	These tests can also be run in automated mode by test programs. This will of
135	course not test the web client, but are useful if one quickly needs to do
136	parts of the test and then continue with, for example, the user or analysis tests
137	on the web.
138	</p>
139
140	<p>
141	The data files needed by the tests are NOT included in the subversion repository.
142	The main reason is that they are too large, and that we don't have permission to
143	make them publicly available for download. To get the test file you need to be a
144	core developer. Read the instructions on the
145	<a href="http://base.thep.lu.se/wiki/DeveloperInformation">DeveloperInformation</a>
146	page, <code>Test data</code> section on the BASE web site. The automated
147	test programs require that file are placed (checked out) in the 'testdata'
148	directory located in the BASE root directory. NOTE! Some test data files are
149	bzip-compressed. Use the automatic unpacking that is built-in to BASE when
150	uploading.
151	</p>
152
153	<p>
154	To run the tests do the following:
155	</p>
156	<ol>
157
158	<li>Compile the core and the test programs: <code>ant main test</code>.</li>
159
160	<li>Change to the <code>build/test/</code> directory.</li>
161
162	<li>Run test programs: <code>./test.sh roles [OPTION] <cmds></code> where
163	<code><cmds></code> is one or more of the following:
164	<ul>
165	<li><code>all</code>: run all tests</li>
166	<li><code>root</code>: run the root user tests</li>
167	<li><code>admin</code>: run the administrator tests</li>
168	<li><code>power</code>: run the power user tests</li>
169	<li><code>user</code>: run the regular user tests</li>
170	<li><code>guest</code>: run the guest user tests</li>
171	</ul>
172	and <code>OPTION</code> can be none or more of:
173	<ul>
174	<li><code>-b</code>: if the batch importers should be tested</li>
175	</ul>
176	</li>
177
178	</ol>
179
180	<a name="root"></a>
181	<h2>2. Root user tests</h2>
182	<p>
183	The root user creates an administrator which is a server-wide admin.
184	</p>
185
186	<ol>
187	<li>
188	Create a new user and set the following
189	properties. All other properties may remain unchanged.
190
191	<table class="listing" cellspacing="0" cellpadding="2" border="0">
192	<tr>
193	<th>Name</th>
194	<th>Login/Password</th>
195	<th>Quota</th>
196	<th>Quota group</th>
197	<th>Membership</th>
198	</tr>
199	<tr>
200	<td>Admin</td>
201	<td>admin/admin</td>
202	<td>Unlimited</td>
203	<td>-</td>
204	<td>Roles: Administrator</td>
205	</tr>
206	</table>
207	</li>
208	</ol>
209
210	<a name="admin"></a>
211	<h2>3. Administrator tests</h2>
212	<p>
213	The administrator creates users for a project and gives them permissions
214	that are suitable for their role in the project. The administrator also
215	sets up quota and group membership.
216	</p>
217
218	<ol>
219	<li>
220	Create a new group and set the following properties:
221
222	<table class="listing" cellspacing="0" cellpadding="2" border="0">
223	<tr>
224	<th>Name</th>
225	<th>Quota</th>
226	</tr>
227	<tr>
228	<td>Group A</td>
229	<td>1GB</td>
230	</tr>
231	</table>
232	<p>
233	</li>
234
235	<li>
236	Create the following users:
237
238	<table class="listing" cellspacing="0" cellpadding="2" border="0">
239	<tr>
240	<th>Name</th>
241	<th>Login/Password</th>
242	<th>Quota</th>
243	<th>Quota group</th>
244	<th>Membership</th>
245	<th>Other</th>
246	</tr>
247	<tr>
248	<td>Power user</td>
249	<td>power/power</td>
250	<td>1GB</td>
251	<td>Group A</td>
252	<td>Roles: Power user</td>
253	<td>-</td>
254	</tr>
255	<tr>
256	<td>User</td>
257	<td>user/user</td>
258	<td>1GB</td>
259	<td>Group A</td>
260	<td>Roles: User</td>
261	<td>-</td>
262	</tr>
263	<tr>
264	<td>Guest</td>
265	<td>guest/guest</td>
266	<td>10MB</td>
267	<td>Group A</td>
268	<td>Roles: Guest</td>
269	<td><i>Multi-user account</i> checked</td>
270	</tr>
271	</table>
272	<p>
273	</li>
274
275	<li>Give USE permission for the listed users to the following plugins:
276
277	<table class="listing" cellspacing="0" cellpadding="2" border="0">
278	<tr>
279	<th>User</th>
280	<th>Plugins</th>
281	</tr>
282	<tr>
283	<td>Power user</td>
284	<td>
285	<ul>
286	<li>Plate importer</li>
287	<li>Reporter map importer</li>
288	<li>Print map importer</li>
289	<li>GTF reporter map importer</li>
290	<li>Array design importer</li>
291	<li>Array batch importer</li>
292	<li>Array slide importer</li>
293	</ul>
294	</td>
295	</tr>
296	</table>
297	<p>
298	</li>
299
300	<li>
301	Create file formats (<i>i.e.</i>, plug-in configurations) for importing
302	reporters. The formats marked as
303	optional are not used in the test procedure, but may be useful to weed
304	out import problems, since they allow importing all info from the raw
305	data files. You may either enter the regular expressions as specified or
306	use the "Test with file" feature.
307
308	<table class="listing" cellspacing="0" cellpadding="2" border="0">
309	<tr>
310	<th>Name</th>
311	<th>Plugin</th>
312	<th>Configuration values</th>
313	</tr>
314	<tr class="oddrow">
315	<td>Reporters for project A</td>
316	<td>Reporter importer</td>
317	<td>
318	<table border="0" cellspacing="0" cellpadding="2">
319	<tr>
320	<td><b>File</b></td>
321	<td><code>mouse/<br>plates_and_reporters.mouse.v4.37k.txt</code></td>
322	</tr>
323	<tr>
324	<td><i>Data header</i></td>
325	<td>384_number\t384_column\t384_row\t384_position\toligo_id.*</td>
326	</tr>
327	<tr>
328	<td><i>Data splitter</i></td>
329	<td>\t</td>
330	</tr>
331	<tr>
332	<td><i>Min data columns</i></td>
333	<td>5</td>
334	</tr>
335	<tr>
336	<td><i>Name</i></td>
337	<td>\oligo_id\</td>
338	</tr>
339	<tr>
340	<td><i>External ID</i></td>
341	<td>\oligo_id\</td>
342	</tr>
343	<tr>
344	<td><i>Description</i></td>
345	<td>\description_Ensembl*\</td>
346	</tr>
347	<tr>
348	<td><i>Gene symbol</i></td>
349	<td>\gene_symbol_Ensembl*\</td>
350	</tr>
351	<tr>
352	<td><i>Sequence</i></td>
353	<td>\oligo_sequence\</td>
354	</tr>
355	</table>
356
357	</td>
358	</tr>
359
360	<tr class="evenrow">
361	<td>GenePix reporter importer<br>(optional)</td>
362	<td>Reporter importer</td>
363	<td>
364
365	<table border="0" cellspacing="0" cellpadding="2">
366	<tr>
367	<td><b>File</b></td>
368	<td><code>mouse/<br>genepix.mouse.v4.37k.00h.gpr</code></td>
369	</tr>
370	<tr>
371	<td><i>Data header</i></td>
372	<td>"Block"\t"Column"\t"Row"\t"Name"\t"ID"\t.*</td>
373	</tr>
374	<tr>
375	<td><i>Data splitter</i></td>
376	<td>\t</td>
377	</tr>
378	<tr>
379	<td><i>Min data columns</i></td>
380	<td>48</td>
381	</tr>
382	<tr>
383	<td><i>Max data columns</i></td>
384	<td>48</td>
385	</tr>
386	<tr>
387	<td><i>Name</i></td>
388	<td>\Name\</td>
389	</tr>
390	<tr>
391	<td><i>External ID</i></td>
392	<td>\ID\</td>
393	</tr>
394	</table>
395
396	</td>
397	</tr>
398	<tr class="oddrow">
399	<td>Reporters from Affymetrix annotations file</td>
400	<td>Reporter importer</td>
401	<td>
402	<table border="0" cellspacing="0" cellpadding="2">
403	<tr>
404	<td><b>File</b></td>
405	<td><code>affymetrix/annotations/<br>MG_U74Av2_annot.csv.bz2</code></td>
406	</tr>
407	<tr>
408	<td><i>Data header</i></td>
409	<td>"Probe Set ID","GeneChip Array".*</td>
410	</tr>
411	<tr>
412	<td><i>Data splitter</i></td>
413	<td>(?!"),(?=")</td>
414	</tr>
415	<tr>
416	<td><i>Name</i></td>
417	<td>\Probe Set ID\</td>
418	</tr>
419	<tr>
420	<td><i>External ID</i></td>
421	<td>\Probe Set ID\</td>
422	</tr>
423	<tr>
424	<td><i>Description</i></td>
425	<td>\Target Description\</td>
426	</tr>
427	<tr>
428	<td><i>Gene symbol</i></td>
429	<td>\Gene Symbol\</td>
430	</tr>
431	</table>
432
433	</td>
434	</tr>
435	<tr class="evenrow">
436	<td>Reporters from GTF file</td>
437	<td>GTF Reporter importer</td>
438	<td>
439
440	<table border="0" cellspacing="0" cellpadding="2">
441	<tr>
442	<td><b>File</b></td>
443	<td><code>sequencing/<br>UCSC_Human_hg19_RefSeqGenes.gtf.tar.bz2</code></td>
444	</tr>
445	<tr>
446	<td><i>Data header</i></td>
447	<td><seqname>\t.<transcript_id>.</td>
448	</tr>
449	<tr>
450	<td><i>Data splitter</i></td>
451	<td>\t</td>
452	</tr>
453	<tr>
454	<td><i>Min data columns</i></td>
455	<td>4</td>
456	</tr>
457	<tr>
458	<td><i>Remove quotes</i></td>
459	<td>yes</td>
460	</tr>
461	<tr>
462	<td><i>Complex mappings</i></td>
463	<td>allow</td>
464	</tr>
465	<tr>
466	<td><i>Name</i></td>
467	<td>\<transcript_id>\@\<seqname>\</td>
468	</tr>
469	<tr>
470	<td><i>External ID</i></td>
471	<td>\<transcript_id>\@\<seqname>\</td>
472	</tr>
473	<tr>
474	<td><i>Gene symbol</i></td>
475	<td>\<gene_id>\</td>
476	</tr>
477	<tr>
478	<td><i>Chromosome</i></td>
479	<td>\<seqname>\</td>
480	</tr>
481	</table>
482
483	</td>
484	</tr>
485	</table>
486	<p>
487	</li>
488
489	<li>
490	Import reporters:
491	<ol>
492	<li>Go to the <code>View -> Reporters</code> page.</li>
493	<li>Click on the <code>Import</code> button.</li>
494	<li>Choose <code>auto-detect</code> and then upload
495	the file <code>plates_and_reporters.mouse.v4.37k.txt</code>.</li>
496	<li>The <code>Reporters for project A</code> format should be
497	found.</li>
498	<li>Select the <code>skip</code> option for the "Missing a required" value
499	since the file contains rows with empty reporter ID:s.
500	<li>Continue and wait for the import to finish. It should create 35,912 new reporters.</li>
501	<li>
502	Repeat the procedure with the <code>MG_U74Av2_annot.csv</code> file. This time
503	also select <code>crop</code> for the "String too long" setting since
504	the file contains data that is too large for the datbase.
505	12,488 new reporters should be created.
506	<li>
507	Repeat the procedure with the <code>UCSC_Human_hg19_RefSeqGenes.gtf</code>
508	file. The default error handling options can be used. This time
509	38,977 new reporters should be created.
510	</ol>
511	<p>
512
513	</li>
514
515
516	</ol>
517
518
519	<a name="power"></a>
520	<h2>4. Power user tests</h2>
521	<p>
522	The power user is the typical owner/administrator of a project. The power user sets
523	up common resources used in the project, such as hardware, software, protocols,
524	file formats and annotation types. In this case the power user is also responsible for
525	managing the LIMS.
526	</p>
527
528	<ol>
529	<li>
530	Create a project:
531
532	<table class="listing" cellspacing="0" cellpadding="2" border="0">
533	<tr>
534	<th>Name</th>
535	<th>Members</th>
536	</tr>
537	<tr>
538	<td>Project A</td>
539	<td>Groups: Group A (Use permission)</td>
540	</tr>
541	</table>
542	<p>
543	</li>
544
545	<li>Activate the project.<p></li>
546
547	<li>
548	Create annotation types [A] and protocol parameters [P]:
549	<table class="listing" cellspacing="0" cellpadding="2" border="0">
550	<tr>
551	<th>Name</th>
552	<th>Type</th>
553	<th>Unit</th>
554	<th>Interface</th>
555	<th>Values</th>
556	<th>Item types</th>
557	</tr>
558	<tr>
559	<td>Drug resistance [A]</td>
560	<td>String</td>
561	<td>-</td>
562	<td>radiobuttons</td>
563	<td>high, medium, low</td>
564	<td>Biosource</td>
565	</tr>
566	<tr>
567	<td>Time [A]</td>
568	<td>Integer</td>
569	<td>Hour</td>
570	<td>text box</td>
571	<td>-</td>
572	<td>Sample</td>
573	</tr>
574	<tr>
575	<td>RIN [A]</td>
576	<td>Float</td>
577	<td>-</td>
578	<td>text box</td>
579	<td>-</td>
580	<td>Extract</td>
581	</tr>
582	<tr>
583	<td>Dye swap [A]</td>
584	<td>Boolean</td>
585	<td>-</td>
586	<td>-</td>
587	<td>-</td>
588	<td>Raw bioassay</td>
589	</tr>
590	<tr>
591	<td>PMT gain [P]</td>
592	<td>Float</td>
593	<td>Volt (Electric potential)</td>
594	<td>-</td>
595	<td>-</td>
596	<td>Derived bioassay</td>
597	</tr>
598	</table>
599	<p>
600	</li>
601
602	<li>
603	Create item subtypes:
604	<table class="listing" cellspacing="0" cellpadding="2" border="0">
605	<tr>
606	<th>Name</th>
607	<th>Item type</th>
608	<th>Push annotations to parent</th>
609	</tr>
610	<tr>
611	<td>Quality control</td>
612	<td>Extract</td>
613	<td>Yes</td>
614	</tr>
615	</table>
616	<p>
617	</li>
618
619	<li>
620	Create protocols (keep the 'Add as project default' option checked and the 'Replace existing default' unchecked):
621	<table class="listing" cellspacing="0" cellpadding="2" border="0">
622	<tr>
623	<th>Name</th>
624	<th>Type</th>
625	<th>Comment</th>
626	</tr>
627	<tr>
628	<td>Sampling A</td>
629	<td>Sampling</td>
630	</tr>
631	<tr>
632	<td>Extraction A</td>
633	<td>Extraction</td>
634	</tr>
635	<tr>
636	<td>Labeling A</td>
637	<td>Labeling</td>
638	</tr>
639	<tr>
640	<td>Library preparation A</td>
641	<td>Library preparation</td>
642	</tr>
643	<tr>
644	<td>Hybridization A</td>
645	<td>Hybridization</td>
646	</tr>
647	<tr>
648	<td>cBot Settings A</td>
649	<td>Cluster generation</td>
650	</tr>
651	<tr>
652	<td>Scanning A</td>
653	<td>Scanning</td>
654	<td>Select 'PMT gain' as a protocol parameter.</td>
655	</tr>
656	<tr>
657	<td>HiSeq Settings A</td>
658	<td>Sequencing</td>
659	</tr>
660	<tr>
661	<td>TopHat Settings A</td>
662	<td>Alignment</td>
663	</tr>
664	<tr>
665	<td>Feature extraction A</td>
666	<td>Feature extraction</td>
667	</tr>
668	<tr>
669	<td>Cufflinks Settings A</td>
670	<td>Feature extraction</td>
671	</tr>
672	<tr>
673	<td>Printing A</td>
674	<td>Printing</td>
675	</tr>
676	</table>
677	<p>
678	</li>
679
680	<li>
681	Create hardware (keep the 'Add as project default' option checked and the 'Replace existing default' unchecked):
682	<table class="listing" cellspacing="0" cellpadding="2" border="0">
683	<tr>
684	<th>Name</th>
685	<th>Type</th>
686	</tr>
687	<tr>
688	<td>Hybridization station A</td>
689	<td>Hybridization station</td>
690	</tr>
691	<tr>
692	<td>cBot A</td>
693	<td>Cluster generator</td>
694	</tr>
695	<tr>
696	<td>HiSeq 2000 A</td>
697	<td>Sequencer</td>
698	</tr>
699	<tr>
700	<td>Scanner A</td>
701	<td>Scanner</td>
702	</tr>
703	<tr>
704	<td>Print robot A</td>
705	<td>Print robot</td>
706	</tr>
707	</table>
708	<p>
709	</li>
710
711	<li>
712	Create software (keep the 'Add as project default' option checked and the 'Replace existing default' unchecked):
713	<table class="listing" cellspacing="0" cellpadding="2" border="0">
714	<tr>
715	<th>Name</th>
716	<th>Type</th>
717	</tr>
718	<tr>
719	<td>Software A</td>
720	<td>Feature extraction</td>
721	</tr>
722	</table>
723	<p>
724	</li>
725
726	<li>
727	Create a reporter clone template:
728	<table class="listing" cellspacing="0" cellpadding="2" border="0">
729	<tr>
730	<th>Name</th>
731	<th>Properties</th>
732	</tr>
733	<tr>
734	<td>Template A</td>
735	<td>External ID, ID, Version, Sequence, Gene symbol</td>
736	</tr>
737	</table>
738	<p>
739	</li>
740
741	<li>
742	Create bioplate type:
743	<table class="listing" cellspacing="0" cellpadding="2" border="0">
744	<tr>
745	<th>Name</th>
746	<th>Biomaterial type</th>
747	<th>Well lock mode</th>
748	</tr>
749	<tr>
750	<td>Bioplate type A</td>
751	<td>Any</td>
752	<td>Unlocked</td>
753	</tr>
754	</table>
755	<p>
756	</li>
757
758	<li>
759	Create file formats (<i>i.e.</i>, plug-in configurations). The formats marked as
760	optional are not used in the test procedure, but may be useful to weed
761	out import problems, since they allow importing all info from the raw
762	data files. You may either enter the regular expressions as specified or
763	use the "Test with file" feature.
764
765	<table class="listing" cellspacing="0" cellpadding="2" border="0">
766	<tr>
767	<th>Name</th>
768	<th>Plugin</th>
769	<th>Configuration values</th>
770	</tr>
771
772	<tr class="oddrow">
773	<td>Plates for project A</td>
774	<td>Plate importer</td>
775	<td>
776
777	<table border="0" cellspacing="0" cellpadding="2">
778	<tr>
779	<td><b>File</b></td>
780	<td><code>mouse/<br>plates_and_reporters.mouse.v4.37k.txt</code></td>
781	</tr>
782	<tr>
783	<td><i>Data header</i></td>
784	<td>384_number\t384_column\t384_row\t384_position\toligo_id.*</td>
785	</tr>
786	<tr>
787	<td><i>Data splitter</i></td>
788	<td>\t</td>
789	</tr>
790	<tr>
791	<td><i>Min data columns</i></td>
792	<td>5</td>
793	</tr>
794	<tr>
795	<td><i>Plate number/name</i></td>
796	<td>\384_number\</td>
797	</tr>
798	<tr>
799	<td><i>Row</i></td>
800	<td>\384_row\</td>
801	</tr>
802	<tr>
803	<td><i>Column</i></td>
804	<td>\384_column\</td>
805	</tr>
806	<tr>
807	<td><i>Reporter ID</i></td>
808	<td>\oligo_id\</td>
809	</tr>
810	</table>
811
812	</td>
813	</tr>
814
815	<tr class="evenrow">
816	<td>GenePix feature importer<br>(optional)</td>
817	<td>Reporter map importer</td>
818	<td>
819
820	<table border="0" cellspacing="0" cellpadding="2">
821	<tr>
822	<td><b>File</b></td>
823	<td><code>mouse/<br>genepix.mouse.v4.37k.00h.gpr</code></td>
824	</tr>
825	<tr>
826	<td><i>Data header</i></td>
827	<td>"Block"\t"Column"\t"Row"\t"Name"\t"ID"\t.*</td>
828	</tr>
829	<tr>
830	<td><i>Data splitter</i></td>
831	<td>\t</td>
832	</tr>
833	<tr>
834	<td><i>Min data columns</i></td>
835	<td>48</td>
836	</tr>
837	<tr>
838	<td><i>Max data columns</i></td>
839	<td>48</td>
840	</tr>
841	<tr>
842	<td><i>Reporter ID</i></td>
843	<td>\ID\</td>
844	</tr>
845	<tr>
846	<td><i>Block</i></td>
847	<td>\Block\</td>
848	</tr>
849	<tr>
850	<td><i>Column</i></td>
851	<td>\Column\</td>
852	</tr>
853	<tr>
854	<td><i>Row</i></td>
855	<td>\Row\</td>
856	</tr>
857	</table>
858
859	</td>
860	</tr>
861
862	<tr class="oddrow">
863	<td>GTF features for project A</td>
864	<td>GTF reporter map importer</td>
865	<td>
866
867	<table border="0" cellspacing="0" cellpadding="2">
868	<tr>
869	<td><b>File</b></td>
870	<td><code>sequencing/<br>UCSC_Human_hg19_RefSeqGenes.gtf</code></td>
871	</tr>
872	<tr>
873	<td><i>Data header</i></td>
874	<td><seqname>\t.<transcript_id>.</td>
875	</tr>
876	<tr>
877	<td><i>Data splitter</i></td>
878	<td>\t</td>
879	</tr>
880	<tr>
881	<td><i>Min data columns</i></td>
882	<td>4</td>
883	</tr>
884	<tr>
885	<td><i>Remove quotes</i></td>
886	<td>yes</td>
887	</tr>
888	<tr>
889	<td><i>Complex mappings</i></td>
890	<td>allow</td>
891	</tr>
892	<tr>
893	<td><i>Reporter ID</i></td>
894	<td>\<transcript_id>\@\<seqname>\</td>
895	</tr>
896	<tr>
897	<td><i>Feature ID</i></td>
898	<td>\<transcript_id>\@\<seqname>\</td>
899	</tr>
900	</table>
901
902	</td>
903	</tr>
904
905	<tr class="evenrow">
906	<td>Raw data for project A</td>
907	<td>Raw data importer</td>
908	<td>
909
910	<table border="0" cellspacing="0" cellpadding="2">
911	<tr>
912	<td><b>File</b></td>
913	<td><code>mouse/<br>genepix.mouse.v4.37k.00h.gpr</code></td>
914	</tr>
915	<tr>
916	<td><i>Raw data type</i></td>
917	<td>Genepix</td>
918	</tr>
919	<tr>
920	<td><i>Header</i></td>
921	<td>"(.+)=(.*)"</td>
922	</tr>
923	<tr>
924	<td><i>Data header</i></td>
925	<td>"Block"\t"Column"\t"Row"\t"Name"\t"ID"\t."Ratio of Medians \(532\/635\)".</td>
926	</tr>
927	<tr>
928	<td><i>Data splitter</i></td>
929	<td>\t</td>
930	</tr>
931	<tr>
932	<td><i>Min data columns</i></td>
933	<td>48</td>
934	</tr>
935	<tr>
936	<td><i>Max data columns</i></td>
937	<td>48</td>
938	</tr>
939
940	<tr>
941	<td><i>Block</i></td>
942	<td>\Block\</td>
943	</tr>
944	<tr>
945	<td><i>Column</i></td>
946	<td>\Column\</td>
947	</tr>
948	<tr>
949	<td><i>Row</i></td>
950	<td>\Row\</td>
951	</tr>
952	<tr>
953	<td><i>X</i></td>
954	<td>\X\</td>
955	</tr>
956	<tr>
957	<td><i>Y</i></td>
958	<td>\Y\</td>
959	</tr>
960	<tr>
961	<td><i>Reporter ID</i></td>
962	<td>\ID\</td>
963	</tr>
964	<tr>
965	<td><i>Spot diameter</i></td>
966	<td>\Dia.\</td>
967	</tr>
968	<tr>
969	<td><i>Channel 1 foreground median</i></td>
970	<td>\F635 Median\</td>
971	</tr>
972	<tr>
973	<td><i>Channel 1 foreground mean</i></td>
974	<td>\F635 Mean\</td>
975	</tr>
976	<tr>
977	<td><i>Channel 1 foreground standard deviation</i></td>
978	<td>\F635 SD\</td>
979	</tr>
980	<tr>
981	<td><i>Channel 1 background median</i></td>
982	<td>\B635 Median\</td>
983	</tr>
984	<tr>
985	<td><i>Channel 1 background mean</i></td>
986	<td>\B635 Mean\</td>
987	</tr>
988	<tr>
989	<td><i>Channel 1 background standard deviation</i></td>
990	<td>\B635 SD\</td>
991	</tr>
992	<tr>
993	<td><i>Percent pixels within 1 standard deviation</i></td>
994	<td>\% > B635+1SD\</td>
995	</tr>
996	<tr>
997	<td><i>Percent pixels within 2 standard deviations</i></td>
998	<td>\% > B635+2SD\</td>
999	</tr>
1000	<tr>
1001	<td><i>Percent saturated pixels</i></td>
1002	<td>\F635 % Sat.\</td>
1003	</tr>
1004	<tr>
1005	<td><i>Channel 2 foreground median</i></td>
1006	<td>\F532 Median\</td>
1007	</tr>
1008	<tr>
1009	<td><i>Channel 2 foreground mean</i></td>
1010	<td>\F532 Mean\</td>
1011	</tr>
1012	<tr>
1013	<td><i>Channel 2 foreground standard deviation</i></td>
1014	<td>\F532 SD\</td>
1015	</tr>
1016	<tr>
1017	<td><i>Channel 2 background median</i></td>
1018	<td>\B532 Median\</td>
1019	</tr>
1020	<tr>
1021	<td><i>Channel 2 background mean</i></td>
1022	<td>\B532 Mean\</td>
1023	</tr>
1024	<tr>
1025	<td><i>Channel 2 background standard deviation</i></td>
1026	<td>\B532 SD\</td>
1027	</tr>
1028	<tr>
1029	<td><i>Percent pixels within 1 standard deviation</i></td>
1030	<td>\% > B532+1SD\</td>
1031	</tr>
1032	<tr>
1033	<td><i>Percent pixels within 2 standard deviations</i></td>
1034	<td>\% > B532+2SD\</td>
1035	</tr>
1036	<tr>
1037	<td><i>Percent saturated pixels</i></td>
1038	<td>\F532 % Sat.\</td>
1039	</tr>
1040	<tr>
1041	<td><i>Foreground pixels</i></td>
1042	<td>\F Pixels\</td>
1043	</tr>
1044	<tr>
1045	<td><i>Background pixels</i></td>
1046	<td>\B Pixels\</td>
1047	</tr>
1048	<tr>
1049	<td><i>Flags</i></td>
1050	<td>\Flags\</td>
1051	</tr>
1052	</table>
1053
1054	</td>
1055	</tr>
1056
1057	<tr class="oddrow">
1058	<td>Raw data for project A (dye-swap)</td>
1059	<td>Raw data importer</td>
1060	<td>
1061
1062	<table border="0" cellspacing="0" cellpadding="2">
1063	<tr>
1064	<td><b>File</b></td>
1065	<td><code>mouse/<br>genepix.mouse.v4.37k.00h.dyeswap.gpr</code></td>
1066	</tr>
1067	<tr>
1068	<td><i>Raw data type</i></td>
1069	<td>Genepix</td>
1070	</tr>
1071	<tr>
1072	<td><i>Header</i></td>
1073	<td>"(.+)=(.*)"</td>
1074	</tr>
1075	<tr>
1076	<td><i>Data header</i></td>
1077	<td>"Block"\t"Column"\t"Row"\t"Name"\t"ID"\t."Ratio of Medians \(635\/532\)".</td>
1078	</tr>
1079	<tr>
1080	<td><i>Data splitter</i></td>
1081	<td>\t</td>
1082	</tr>
1083	<tr>
1084	<td><i>Min data columns</i></td>
1085	<td>48</td>
1086	</tr>
1087	<tr>
1088	<td><i>Max data columns</i></td>
1089	<td>48</td>
1090	</tr>
1091
1092	<tr>
1093	<td><i>Block</i></td>
1094	<td>\Block\</td>
1095	</tr>
1096	<tr>
1097	<td><i>Column</i></td>
1098	<td>\Column\</td>
1099	</tr>
1100	<tr>
1101	<td><i>Row</i></td>
1102	<td>\Row\</td>
1103	</tr>
1104	<tr>
1105	<td><i>X</i></td>
1106	<td>\X\</td>
1107	</tr>
1108	<tr>
1109	<td><i>Y</i></td>
1110	<td>\Y\</td>
1111	</tr>
1112	<tr>
1113	<td><i>Reporter ID</i></td>
1114	<td>\ID\</td>
1115	</tr>
1116	<tr>
1117	<td><i>Spot diameter</i></td>
1118	<td>\Dia.\</td>
1119	</tr>
1120	<tr>
1121	<td><i>Channel 1 foreground median</i></td>
1122	<td>\F532 Median\</td>
1123	</tr>
1124	<tr>
1125	<td><i>Channel 1 foreground mean</i></td>
1126	<td>\F532 Mean\</td>
1127	</tr>
1128	<tr>
1129	<td><i>Channel 1 foreground standard deviation</i></td>
1130	<td>\F532 SD\</td>
1131	</tr>
1132	<tr>
1133	<td><i>Channel 1 background median</i></td>
1134	<td>\B532 Median\</td>
1135	</tr>
1136	<tr>
1137	<td><i>Channel 1 background mean</i></td>
1138	<td>\B532 Mean\</td>
1139	</tr>
1140	<tr>
1141	<td><i>Channel 1 background standard deviation</i></td>
1142	<td>\B532 SD\</td>
1143	</tr>
1144	<tr>
1145	<td><i>Percent pixels within 1 standard deviation</i></td>
1146	<td>\% > B532+1SD\</td>
1147	</tr>
1148	<tr>
1149	<td><i>Percent pixels within 2 standard deviations</i></td>
1150	<td>\% > B532+2SD\</td>
1151	</tr>
1152	<tr>
1153	<td><i>Percent saturated pixels</i></td>
1154	<td>\F532 % Sat.\</td>
1155	</tr>
1156	<tr>
1157	<td><i>Channel 2 foreground median</i></td>
1158	<td>\F635 Median\</td>
1159	</tr>
1160	<tr>
1161	<td><i>Channel 2 foreground mean</i></td>
1162	<td>\F635 Mean\</td>
1163	</tr>
1164	<tr>
1165	<td><i>Channel 2 foreground standard deviation</i></td>
1166	<td>\F635 SD\</td>
1167	</tr>
1168	<tr>
1169	<td><i>Channel 2 background median</i></td>
1170	<td>\B635 Median\</td>
1171	</tr>
1172	<tr>
1173	<td><i>Channel 2 background mean</i></td>
1174	<td>\B635 Mean\</td>
1175	</tr>
1176	<tr>
1177	<td><i>Channel 2 background standard deviation</i></td>
1178	<td>\B635 SD\</td>
1179	</tr>
1180	<tr>
1181	<td><i>Percent pixels within 1 standard deviation</i></td>
1182	<td>\% > B635+1SD\</td>
1183	</tr>
1184	<tr>
1185	<td><i>Percent pixels within 2 standard deviations</i></td>
1186	<td>\% > B635+2SD\</td>
1187	</tr>
1188	<tr>
1189	<td><i>Percent saturated pixels</i></td>
1190	<td>\F635 % Sat.\</td>
1191	</tr>
1192	<tr>
1193	<td><i>Foreground pixels</i></td>
1194	<td>\F Pixels\</td>
1195	</tr>
1196	<tr>
1197	<td><i>Background pixels</i></td>
1198	<td>\B Pixels\</td>
1199	</tr>
1200	<tr>
1201	<td><i>Flags</i></td>
1202	<td>\Flags\</td>
1203	</tr>
1204	</table>
1205
1206	</td>
1207	</tr>
1208	</table>
1209	<p>
1210	</li>
1211
1212	<li>
1213	Annotate the file formats:
1214	<table class="listing" cellspacing="0" cellpadding="2" border="0">
1215	<tr>
1216	<th>File format</th>
1217	<th>Annotation</th>
1218	<th>Value</th>
1219	</tr>
1220	<tr>
1221	<td>Raw data for project A</td>
1222	<td>Dye swap</td>
1223	<td>false</td>
1224	</tr>
1225	<tr>
1226	<td>Raw data for project A (dye swap)</td>
1227	<td>Dye swap</td>
1228	<td>true</td>
1229	</tr>
1230	</table>
1231	This will make the raw data importer automatically annotate the
1232	raw bioassays with the specified annotations.
1233	<p>
1234	</li>
1235
1236	<li>
1237	Create plate type:
1238	<table class="listing" cellspacing="0" cellpadding="2" border="0">
1239	<tr>
1240	<th>Name</th>
1241	<th>Geometry</th>
1242	</tr>
1243	<tr>
1244	<td>Plate type A</td>
1245	<td>384-well (16 x 24)</td>
1246	</tr>
1247	</table>
1248	<p>
1249	</li>
1250
1251	<li>
1252	Import plates:
1253	<ol>
1254	<li>Go to the <code>Array LIMS -> Plates</code> page.</li>
1255	<li>Click on the <code>Import</code> button.</li>
1256	<li>Choose <code>auto-detect</code> and select
1257	the file <code>plates_and_reporters.mouse.v4.37k.txt</code>.</li>
1258	<li>The <code>Plates for project A</code> format should be
1259	found.</li>
1260	<li>Specify the following parameters:
1261
1262	<table border="0" cellspacing="0" cellpadding="2">
1263	<tr>
1264	<td><i>Plate type</i></td>
1265	<td>Plate type A</td>
1266	</tr>
1267	<tr>
1268	<td><i>Plate name prefix</i></td>
1269	<td>Plate A</td>
1270	</tr>
1271	<tr>
1272	<td><i>Plate name padding</i></td>
1273	<td>4</td>
1274	</tr>
1275	</table>
1276	</li>
1277	<li>Continue and wait for the import to finish. It should create 96 plates.</li>
1278	</ol>
1279	<p>
1280	</li>
1281
1282	<li>
1283	Create array designs and upload data files to them. Keep the 'Set as project default' option checked
1284	if doing this manually.
1285	<table class="listing" cellspacing="0" cellpadding="2" border="0">
1286	<tr>
1287	<th>Name</th>
1288	<th>Platform/Variant</th>
1289	<th>File(s)</th>
1290	</tr>
1291	<tr>
1292	<td>Array design A</td>
1293	<td>Generic</td>
1294	<td><i>Print map</i>: <code>mouse/printmap.mouse.v4.37k.tam</code></td>
1295	</tr>
1296	<tr>
1297	<td>Affymetrix A</td>
1298	<td>Affymetrix</td>
1299	<td><i>CDF file</i>: <code>affymtrix/cdf/MG_U74Av2.cdf</code></td>
1300	</tr>
1301	<tr>
1302	<td>RefSeqDesign A</td>
1303	<td>Sequencing/Expression-like</td>
1304	<td><i>GTF ref-seq file</i>: <code>sequencing/UCSC_Human_hg19_RefSeqGenes.gtf</code></td>
1305	</tr>
1306	</table>
1307	<p>
1308	Or
1309	<p>
1310	Import array designs with the ArrayDesignImporter plug-in.
1311	<ol>
1312	<li>Make sure the data-files, mentioned in table above, are located in <code>/home/power/</code>, upload them if not</li>
1313	<li>Click on the <code>Import</code> button on the array design list page.</li>
1314	<li>Choose ArrayDesignImporter in the plug-in drop-down list.</li>
1315	<li><b>Test with file:</b> <code>arraydesign_out.txt</code> and set
1316	the parsing parameters with help of the <code>Auto generate</code> button on the <code>Column mapping</code>
1317	tab.</li>
1318	<li>Start the import-job by clicking on the <code>Finish</code> button on the third wizard-page.</li>
1319	</ol>
1320	<p>
1321	</li>
1322
1323	<li>
1324	Connect <code>Array design A</code> with plates. Select the imported plates (plate names starting
1325	with <code>Plate A</code>) and sort them in the correct order (as indicated by their names).
1326	<p>
1327	</li>
1328
1329	<li>
1330	Import features to Array design A:
1331	<ol>
1332	<li>Click on the <code>Import</code> button when viewing properties for the array design.</li>
1333	<li>Choose <code>auto-detect</code> and use the file
1334	<code>printmap.mouse.v4.37k.tam</code>.</li>
1335	<li>The <code>Print map importer</code> plug-in should be
1336	found.</li>
1337	<li>Continue and wait for the import to finish. It should create 36,864 features and 48 blocks.</li>
1338	</ol>
1339	<p>
1340	Import features to RefSeqDesign A:
1341	<ol>
1342	<li>Click on the <code>Import</code> button when viewing properties for the array design.</li>
1343	<li>Choose <code>auto-detect</code> and use the file
1344	<code>UCSC_Human_hg19_RefSeqGenes.gtf</code>.</li>
1345	<li>The <code>GTF reporter map importer</code> plug-in should be
1346	found. Select the <code>GTF features for project A</code> format.</li>
1347	<li>Continue and wait for the import to finish. It should create 38,977 features and 1 block.</li>
1348	</ol>
1349	<p>
1350	</li>
1351
1352	<li>
1353	Set project defaults. Go to the projects page and edit the
1354	<code>Project A</code> project. On the <code>Defaults</code>
1355	tab, set the following defaults. NOTE! Most of the items in this
1356	list should already be registered as default items if the
1357	'Add as project default' option was used when creating the new items.
1358
1359	<table class="listing" cellspacing="0" cellpadding="2" border="0">
1360	<tr>
1361	<th>Setting</th>
1362	<th>Value(s)</th>
1363	</tr>
1364	<tr>
1365	<td>Raw data type</td>
1366	<td>Genepix</td>
1367	</tr>
1368	<tr>
1369	<td>Platforms</td>
1370	<td>
1371	Generic<br>
1372	Affymetrix
1373	</td>
1374	</tr>
1375	<tr>
1376	<td>Platforms variants</td>
1377	<td>
1378	Sequencing / Expression-like
1379	</td>
1380	</tr>
1381	<tr>
1382	<td>Array designs</td>
1383	<td>
1384	Array design A<br>
1385	Affymetrix A<br>
1386	RefSeqDesign A
1387	</td>
1388	</tr>
1389	<tr>
1390	<td>Protocols</td>
1391	<td>
1392	Sampling A<br>
1393	Extraction A<br>
1394	Labeling A<br>
1395	Library preparation A<br>
1396	Hybridization A<br>
1397	cBot Settings A<br>
1398	Scanning A<br>
1399	HiSeq Settings A<br>
1400	TopHat Settings A<br>
1401	Feature extraction A<br>
1402	Cufflinks Settings A<br>
1403	Printing A
1404	</td>
1405	</tr>
1406	<tr>
1407	<td>Hardware</td>
1408	<td>
1409	Hybridization station A<br>
1410	cBot A<br>
1411	HiSeq 2000 A<br>
1412	Scanner A<br>
1413	Print robot A
1414	</td>
1415	</tr>
1416	<tr>
1417	<td>Software</td>
1418	<td>
1419	Software A<br>
1420	TopHat<br>
1421	Cufflinks
1422	</td>
1423	</tr>
1424	</table>
1425
1426	<p>
1427	</li>
1428
1429	<li>
1430	Create array batches:
1431	<table class="listing" cellspacing="0" cellpadding="2" border="0">
1432	<tr>
1433	<th>Name</th>
1434	<th>Array design</th>
1435	<th>Print robot</th>
1436	<th>Protocol</th>
1437	</tr>
1438	<tr>
1439	<td>Array batch A</td>
1440	<td>Array design A</td>
1441	<td>Print robot A</td>
1442	<td>Printing A</td>
1443	</tr>
1444	<tr>
1445	<td>Affymetrix batch A</td>
1446	<td>Affymetrix A</td>
1447	<td></td>
1448	<td></td>
1449	</tr>
1450	</table>
1451	<p>
1452	Or
1453	<p>
1454	Import array batches with the ArrayBatchImporter plug-in.
1455	<ol>
1456	<li>Click on the <code>Import</code> button on the array batch list page.</li>
1457	<li>Select ArrayBatchImporter in the plug-in drop-down list and click <code>Next</code></li>
1458	<li><b>Test with file:</b> <code>arraybatch_out.txt</code> and set the parsing parameters
1459	with help of the <code>Auto generate</code> button on the <code>Column mapping</code>
1460	tab.</li>
1461	<li>Start the import-job by clicking on the <code>Finish</code> button on the third wizzard-page.</li>
1462	</ol>
1463	<p>
1464	</li>
1465
1466	<li>
1467	Create array slides with the <code>Create slides</code>
1468	wizard.
1469
1470	<table class="listing" cellspacing="0" cellpadding="2" border="0">
1471	<tr>
1472	<th>Name</th>
1473	<th>Array batch</th>
1474	<th>Quantity</th>
1475	</tr>
1476	<tr>
1477	<td>Array slide A.</td>
1478	<td>Array batch A</td>
1479	<td>4</td>
1480	</tr>
1481	<tr>
1482	<td>Affymetrix slide A.</td>
1483	<td>Affymetrix batch A</td>
1484	<td>3</td>
1485	</tr>
1486	</table>
1487	<p>
1488	Or
1489	<p>
1490	Import array slides with the ArraySlideImporter plug-in.
1491	<ol>
1492	<li>Click on the <code>Import</code> button on the array slide list page.</li>
1493	<li>Select ArraySlideImporter in the plug-in drop-down list and click <code>Next</code></li>
1494	<li><b>Test with file:</b> <code>arrayslide_out.txt</code> and set the parsing parameters
1495	with help of the <code>Auto generate</code> button on the <code>Column mapping</code>
1496	tab.</li>
1497	<li>Start the import-job by clicking on the <code>Finish</code> button on the third wizzard-page.</li>
1498	</ol>
1499	<p>
1500	</li>
1501	</ol>
1502
1503	<a name="user"></a>
1504	<h2>5. User tests</h2>
1505	<p>
1506	The user is a typical worker in the project. The user does the actual experimentation in the
1507	lab, which includes collecting samples, doing extraction, labeling and hybridizations.
1508	The user also scans and analyses the raw data resulting from the images. Inserting items can be
1509	done in two different ways, .
1510	</p>
1511	<h3>First step</h3>
1512
1513	<ol>
1514	<li>Activate the <code>Project A</code> project.
1515	<p>
1516
1517	<li>
1518	Create a bioplate:
1519	<table class="listing" cellspacing="0" cellpadding="2" border="0">
1520	<tr>
1521	<th>Name</th>
1522	<th>Plate geometry</th>
1523	<th>Bioplate type</th>
1524	</tr>
1525	<tr>
1526	<td>Bioplate A</td>
1527	<td>96-well (8 x 12)</td>
1528	<td>BioPlate type A</td>
1529	</tr>
1530	</table>
1531	<p>
1532	<li>Continue with the second step, which can be done with batch importers or
1533	manually.
1534
1535	</ol>
1536
1537
1538	<h3>Second step (using batch importers)</h3>
1539
1540	<ol>
1541	<li>Click on the <code>Import</code> button on the list page.</li>
1542	<li>Select <itemtype>Importer in the plug-in drop-down list and click <code>Next</code></li>
1543	<li><b>Test with file:</b> using the right file(listed below) and set the parsing parameters
1544	by using the <code>Auto generate</code> button on the <code>Column mapping</code> tab.
1545	<table class="listing" cellspacing="0" cellpadding="2" border="0">
1546	<tr>
1547	<th>Itemtype</th>
1548	<th>File</th>
1549	</tr>
1550	<tr>
1551	<td>Biosource</td>
1552	<td>biosource_out.txt</td>
1553	</tr>
1554	<tr>
1555	<td>Samples</td>
1556	<td>sample_out.txt</td>
1557	</tr>
1558	<tr>
1559	<td>Extracts (including labeled extracts and libraries)</td>
1560	<td>extract_out.txt</td>
1561	</tr>
1562	<tr>
1563	<td>Physical bioassays (hybridizations, flow cells)</td>
1564	<td>physicalbioassay_out.txt</td>
1565	</tr>
1566	<tr>
1567	<td>Derived bioassays (scans, assemblys)</td>
1568	<td>derivedbioassay_out.txt</td>
1569	</tr>
1570	<tr>
1571	<td>Raw bioassays</td>
1572	<td>rawbioassay_out.txt</td>
1573	</tr>
1574	</table>
1575	The files listed for biosource, samples, extracts, and derived bioassays also contain annotations
1576	for the items and these files should also be used with the annotation importer.
1577	The procedure is the same as for batch importers except that only <code>\Name\</code>
1578	is needed in the column mapping. The annotation column should be selected by default in
1579	the second wizard-step.
1580	</li>
1581	<li>Start the import-job by clicking on the <code>Finish</code> button on the third wizard-page.</li>
1582	<li>Continue with <a href="#step3">the third step</a>.</li>
1583	</ol>
1584
1585	<h3>Second step (create items manually)</h3>
1586	<ol>
1587	<li>
1588	Create a biosource:
1589	<table class="listing" cellspacing="0" cellpadding="2" border="0">
1590	<tr>
1591	<th>Name</th>
1592	<th>Annotations</th>
1593	</tr>
1594	<tr>
1595	<td>Biosource A</td>
1596	<td>
1597	<table border="0" cellspacing="0" cellpadding="2">
1598	<tr>
1599	<td><i>Drug resistance:</i></td>
1600	<td>medium</td>
1601	</tr>
1602	</table>
1603	</td>
1604	</tr>
1605	</table>
1606	<p>
1607	</li>
1608
1609	<li>
1610	Create samples:
1611	<table class="listing" cellspacing="0" cellpadding="2" border="0">
1612	<tr>
1613	<th>Name</th>
1614	<th>Protocol</th>
1615	<th>Biosource</th>
1616	<th>Bioplate [well]</th>
1617	<th>Annotations</th>
1618	</tr>
1619	<tr>
1620	<td>Sample A.00h</td>
1621	<td>Sampling A</td>
1622	<td>Biosource A</td>
1623	<td>Bioplate A [A1]</td>
1624	<td>
1625	<table border="0" cellspacing="0" cellpadding="2">
1626	<tr>
1627	<td><i>Time:</i></td>
1628	<td>0h</td>
1629	</tr>
1630	</table>
1631	</td>
1632	</tr>
1633	<tr>
1634	<td>Sample A.24h</td>
1635	<td>Sampling A</td>
1636	<td>Biosource A</td>
1637	<td>Bioplate A [A2]</td>
1638	<td>
1639	<table border="0" cellspacing="0" cellpadding="2">
1640	<tr>
1641	<td><i>Time:</i></td>
1642	<td>24h</td>
1643	</tr>
1644	</table>
1645	</td>
1646	</tr>
1647	<tr>
1648	<td>Sample A.ref</td>
1649	<td>Sampling A</td>
1650	<td>-</td>
1651	<td>Bioplate A [A3]</td>
1652	<td>-</td>
1653	</tr>
1654	</table>
1655	<p>
1656	</li>
1657
1658	<li>
1659	Create extracts:
1660	<table class="listing" cellspacing="0" cellpadding="2" border="0">
1661	<tr>
1662	<th>Name</th>
1663	<th>Type</th>
1664	<th>Protocol</th>
1665	<th>Parent</th>
1666	<th>Bioplate [well]</th>
1667	<th>Annotations</th>
1668	</tr>
1669	<tr>
1670	<td>Extract A.00h</td>
1671	<td>-</td>
1672	<td>Extraction A</td>
1673	<td>Sample A.00h</td>
1674	<td>Bioplate A [B1]</td>
1675	<td>-</td>
1676	</tr>
1677	<tr>
1678	<td>Extract A.24h</td>
1679	<td>-</td>
1680	<td>Extraction A</td>
1681	<td>Sample A.24h</td>
1682	<td>Bioplate A [B2]</td>
1683	<td>-</td>
1684	</tr>
1685	<tr>
1686	<td>Extract A.ref</td>
1687	<td>-</td>
1688	<td>Extraction A</td>
1689	<td>Sample A.ref</td>
1690	<td>Bioplate A [B3]</td>
1691	<td>-</td>
1692	</tr>
1693	<tr>
1694	<td>Extract A.00h.qc</td>
1695	<td>Quality control</td>
1696	<td>-</td>
1697	<td>Extract A.00h</td>
1698	<td>-</td>
1699	<td>
1700	<table border="0" cellspacing="0" cellpadding="2">
1701	<tr>
1702	<td><i>RIN:</i></td>
1703	<td>8.1</td>
1704	</tr>
1705	</table>
1706	</td>
1707	</tr>
1708	<tr>
1709	<td>Extract A.24h.qc</td>
1710	<td>Quality control</td>
1711	<td>-</td>
1712	<td>Extract A.24h</td>
1713	<td>-</td>
1714	<td>
1715	<table border="0" cellspacing="0" cellpadding="2">
1716	<tr>
1717	<td><i>RIN:</i></td>
1718	<td>8.5</td>
1719	</tr>
1720	</table>
1721	</td>
1722	</tr>
1723	<tr>
1724	<td>Extract A.ref.qc</td>
1725	<td>Quality control</td>
1726	<td>-</td>
1727	<td>Extract A.ref</td>
1728	<td>-</td>
1729	<td>
1730	<table border="0" cellspacing="0" cellpadding="2">
1731	<tr>
1732	<td><i>RIN:</i></td>
1733	<td>9.2</td>
1734	</tr>
1735	</table>
1736	</td>
1737	</tr>
1738	</table>
1739	<p>
1740	</li>
1741
1742	<li>
1743	Create labeled extracts and libraries:
1744	<table class="listing" cellspacing="0" cellpadding="2" border="0">
1745	<tr>
1746	<th>Name</th>
1747	<th>Type</th>
1748	<th>Label</th>
1749	<th>Protocol</th>
1750	<th>Extract</th>
1751	<th>Bioplate [well]</th>
1752	</tr>
1753	<tr>
1754	<td>Labeled extract A.00h</td>
1755	<td>Labeled extract</td>
1756	<td>cy3</td>
1757	<td>Labeling A</td>
1758	<td>Extract A.00h</td>
1759	<td>Bioplate A [C1]</td>
1760	</tr>
1761	<tr>
1762	<td>Labeled extract A.24h</td>
1763	<td>Labeled extract</td>
1764	<td>cy3</td>
1765	<td>Labeling A</td>
1766	<td>Extract A.24h</td>
1767	<td>Bioplate A [C2]</td>
1768	</tr>
1769	<tr>
1770	<td>Labeled extract A.ref</td>
1771	<td>Labeled extract</td>
1772	<td>cy5</td>
1773	<td>Labeling A</td>
1774	<td>Extract A.ref</td>
1775	<td>Bioplate A [C3]</td>
1776	</tr>
1777	<tr class="shaded">
1778	<td>Labeled extract A.00h (dye-swap)</td>
1779	<td>Labeled extract</td>
1780	<td>cy5</td>
1781	<td>Labeling A</td>
1782	<td>Extract A.00h</td>
1783	<td>Bioplate A [D1]</td>
1784	</tr>
1785	<tr class="shaded">
1786	<td>Labeled extract A.24h (dye-swap)</td>
1787	<td>Labeled extract</td>
1788	<td>cy5</td>
1789	<td>Labeling A</td>
1790	<td>Extract A.24h</td>
1791	<td>Bioplate A [D2]</td>
1792	</tr>
1793	<tr class="shaded">
1794	<td>Labeled extract A.ref (dye-swap)</td>
1795	<td>Labeled extract</td>
1796	<td>cy3</td>
1797	<td>Labeling A</td>
1798	<td>Extract A.ref</td>
1799	<td>Bioplate A [D3]</td>
1800	</tr>
1801	<tr>
1802	<td>Library A.00h</td>
1803	<td>Library</td>
1804	<td>-</td>
1805	<td>Library preparation A</td>
1806	<td>Extract A.00h</td>
1807	<td>Bioplate A [E1]</td>
1808	</tr>
1809	<tr>
1810	<td>Library A.24h</td>
1811	<td>Library</td>
1812	<td>-</td>
1813	<td>Library preparation A</td>
1814	<td>Extract A.24h</td>
1815	<td>Bioplate A [E2]</td>
1816	</tr>
1817	</table>
1818	<p>
1819	</li>
1820
1821	<li>
1822	Create physical bioassays (hybridizations and flow cells):
1823	<table class="listing" cellspacing="0" cellpadding="2" border="0">
1824	<tr>
1825	<th>Name</th>
1826	<th>Protocol</th>
1827	<th>Hardware</th>
1828	<th>Array slide</th>
1829	<th>Extracts (position)</th>
1830	</tr>
1831	<tr>
1832	<td>Hybridization A.00h</td>
1833	<td>Hybridization A</td>
1834	<td>Hybridization station A</td>
1835	<td>Array slide A.1</td>
1836	<td>Labeled extract A.00h,<br>Labeled extract A.ref</td>
1837	</tr>
1838	<tr>
1839	<td>Hybridization A.24h</td>
1840	<td>Hybridization A</td>
1841	<td>Hybridization station A</td>
1842	<td>Array slide A.2</td>
1843	<td>Labeled extract A.24h,<br>Labeled extract A.ref</td>
1844	</tr>
1845	<tr class="shaded">
1846	<td>Hybridization A.00h (dye-swap)</td>
1847	<td>Hybridization A</td>
1848	<td>Hybridization station A</td>
1849	<td>Array slide A.3</td>
1850	<td>Labeled extract A.00h (dye-swap),<br>Labeled extract A.ref (dye-swap)</td>
1851	</tr>
1852	<tr class="shaded">
1853	<td>Hybridization A.24h (dye-swap)</td>
1854	<td>Hybridization A</td>
1855	<td>Hybridization station A</td>
1856	<td>Array slide A.4</td>
1857	<td>Labeled extract A.24h (dye-swap),<br>Labeled extract A.ref (dye-swap)</td>
1858	</tr>
1859	<tr>
1860	<td>Affymetrix hyb A.1</td>
1861	<td>Hybridization A</td>
1862	<td>Hybridization station A</td>
1863	<td>Affymetrix slide A.1</td>
1864	<td>Labeled extract A.00h</td>
1865	</tr>
1866	<tr>
1867	<td>Affymetrix hyb A.2</td>
1868	<td>Hybridization A</td>
1869	<td>Hybridization station A</td>
1870	<td>Affymetrix slide A.2</td>
1871	<td>Labeled extract A.24h</td>
1872	</tr>
1873	<tr>
1874	<td>Affymetrix hyb A.3</td>
1875	<td>Hybridization A</td>
1876	<td>Hybridization station A</td>
1877	<td>Affymetrix slide A.3</td>
1878	<td>Labeled extract A.ref</td>
1879	</tr>
1880	<tr class="shaded">
1881	<td>Flow cell A</td>
1882	<td>cBot Settings A</td>
1883	<td>cBot A</td>
1884	<td>-</td>
1885	<td>Library A.00h (1),<br>Library A.24h (2)</td>
1886	</tr>
1887	</table>
1888	<p>
1889	</li>
1890
1891	<li>
1892	Create derived bioassays (scans, arrangements, etc.):
1893	<table class="listing" cellspacing="0" cellpadding="2" border="0">
1894	<tr>
1895	<th>Name</th>
1896	<th>Parent bioasasay</th>
1897	<th>Parent extract</th>
1898	<th>Hardware/Software</th>
1899	<th>Protocol</th>
1900	<th>PMT gain</th>
1901	</tr>
1902	<tr>
1903	<td>Scan A.00h</td>
1904	<td>Hybridization A.00h</td>
1905	<td>-</td>
1906	<td>HW: Scanner A</td>
1907	<td>Scanning A</td>
1908	<td>400 V</td>
1909	</tr>
1910	<tr>
1911	<td>Scan A.24h</td>
1912	<td>Hybridization A.24h</td>
1913	<td>-</td>
1914	<td>HW: Scanner A</td>
1915	<td>Scanning A</td>
1916	<td>500 V</td>
1917	</tr>
1918	<tr class="shaded">
1919	<td>Scan A.00h (dye-swap)</td>
1920	<td>Hybridization A.00h (dye-swap)</td>
1921	<td>-</td>
1922	<td>HW: Scanner A</td>
1923	<td>Scanning A</td>
1924	<td>600 V</td>
1925	</tr>
1926	<tr class="shaded">
1927	<td>Scan A.24h (dye-swap)</td>
1928	<td>Hybridization A.24h (dye-swap)</td>
1929	<td>-</td>
1930	<td>HW: Scanner A</td>
1931	<td>Scanning A</td>
1932	<td>700 V</td>
1933	</tr>
1934	<tr>
1935	<td>Affymetrix scan A.1</td>
1936	<td>Affymetrix hyb A.1</td>
1937	<td>-</td>
1938	<td>HW: Scanner A</td>
1939	<td>Scanning A</td>
1940	<td>800 V</td>
1941	</tr>
1942	<tr>
1943	<td>Affymetrix scan A.2</td>
1944	<td>Affymetrix hyb A.2</td>
1945	<td>-</td>
1946	<td>HW: Scanner A</td>
1947	<td>Scanning A</td>
1948	<td>900 V</td>
1949	</tr>
1950	<tr>
1951	<td>Affymetrix scan A.3</td>
1952	<td>Affymetrix hyb A.3</td>
1953	<td>-</td>
1954	<td>HW: Scanner A</td>
1955	<td>Scanning A</td>
1956	<td>1000 V</td>
1957	</tr>
1958	<tr class="shaded">
1959	<td>Sequenced A</td>
1960	<td>Flow cell A</td>
1961	<td>-</td>
1962	<td>HW: HiSeq 2000 A</td>
1963	<td>HiSeq Settings A</td>
1964	<td>-</td>
1965	</tr>
1966	<tr class="shaded">
1967	<td>Arrangement A.00h</td>
1968	<td>Sequenced A</td>
1969	<td>Library A.00h</td>
1970	<td>SW: TopHat</td>
1971	<td>TopHat Settings A</td>
1972	<td>-</td>
1973	</tr>
1974	<tr class="shaded">
1975	<td>Arrangement A.24h</td>
1976	<td>Sequenced A</td>
1977	<td>Library A.24h</td>
1978	<td>SW: TopHat</td>
1979	<td>TopHat Settings A</td>
1980	<td>-</td>
1981	</tr>
1982	</table>
1983	<p>
1984	</li>
1985
1986	<li>
1987	Create raw bioassays:
1988	<table class="listing" cellspacing="0" cellpadding="2" border="0">
1989	<tr>
1990	<th>Name</th>
1991	<th>Platform/Raw data type</th>
1992	<th>Parent bioassay</th>
1993	<th>Parent extract</th>
1994	<th>Array design</th>
1995	<th>Protocol</th>
1996	<th>Software</th>
1997	<th>File(s)</th>
1998	</tr>
1999	<tr>
2000	<td>Raw bioassay A.00h</td>
2001	<td>Generic/GenePix</td>
2002	<td>Scan A.00h</td>
2003	<td>-</td>
2004	<td>Array design A</td>
2005	<td>Feature extraction A</td>
2006	<td>Software A</td>
2007	<td><i>Raw data</i>: <code>mouse/genepix.mouse.v4.37k.00h.gpr</code></td>
2008	</tr>
2009	<tr>
2010	<td>Raw bioassay A.24h</td>
2011	<td>Generic/GenePix</td>
2012	<td>Scan A.24h</td>
2013	<td>-</td>
2014	<td>Array design A</td>
2015	<td>Feature extraction A</td>
2016	<td>Software A</td>
2017	<td><i>Raw data</i>: <code>mouse/genepix.mouse.v4.37k.24h.gpr</code></td>
2018	</tr>
2019	<tr class="shaded">
2020	<td>Raw bioassay A.00h (dye-swap)</td>
2021	<td>Generic/GenePix</td>
2022	<td>Scan A.00h (dye-swap)</td>
2023	<td>-</td>
2024	<td>Array design A</td>
2025	<td>Feature extraction A</td>
2026	<td>Software A</td>
2027	<td><i>Raw data</i>: <code>mouse/genepix.mouse.v4.37k.00h.dyeswap.gpr</code></td>
2028	</tr>
2029	<tr class="shaded">
2030	<td>Raw bioassay A.24h (dye-swap)</td>
2031	<td>Generic/GenePix</td>
2032	<td>Scan A.24h (dye-swap)</td>
2033	<td>-</td>
2034	<td>Array design A</td>
2035	<td>Feature extraction A</td>
2036	<td>Software A</td>
2037	<td><i>Raw data</i>: <code>mouse/genepix.mouse.v4.37k.24h.dyeswap.gpr</code></td>
2038	</tr>
2039	<tr>
2040	<td>Affymetrix raw A.1</td>
2041	<td>Affymetrix</td>
2042	<td>Affymetrix scan A.1</td>
2043	<td>-</td>
2044	<td>Affymetrix A</td>
2045	<td>Feature extraction A</td>
2046	<td>Software A</td>
2047	<td><i>CEL file</i>: <code>affymetrix/E-TEST-1.ebi.ac.uk/jos1761.cel</code></td>
2048	</tr>
2049	<tr>
2050	<td>Affymetrix raw A.2</td>
2051	<td>Affymetrix</td>
2052	<td>Affymetrix scan A.2</td>
2053	<td>-</td>
2054	<td>Affymetrix A</td>
2055	<td>Feature extraction A</td>
2056	<td>Software A</td>
2057	<td><i>CEL file</i>: <code>affymetrix/E-TEST-1.ebi.ac.uk/jos1762.cel</code></td>
2058	</tr>
2059	<tr>
2060	<td>Affymetrix raw A.3</td>
2061	<td>Affymetrix</td>
2062	<td>Affymetrix scan A.3</td>
2063	<td>-</td>
2064	<td>Affymetrix A</td>
2065	<td>Feature extraction A</td>
2066	<td>Software A</td>
2067	<td><i>CEL file</i>: <code>affymetrix/E-TEST-1.ebi.ac.uk/jos1763.cel</code></td>
2068	</tr>
2069	<tr class="shaded">
2070	<td>SeqRaw A.00h</td>
2071	<td>Sequencing/Expression-like/Cufflinks</td>
2072	<td>Arrangement A.00h</td>
2073	<td>Library A.00h</td>
2074	<td>RefSeqDesign A</td>
2075	<td>Cufflinks Settings A</td>
2076	<td>Cufflinks</td>
2077	<td><i>FPKM tracking file</i>: <code>sequencing/dataset1_norm1/isoforms.fpkm_tracking</code></td>
2078	</tr>
2079	<tr class="shaded">
2080	<td>SeqRaw A.24h</td>
2081	<td>Sequencing/Expression-like/Cufflinks</td>
2082	<td>Arrangement A.24h</td>
2083	<td>Library A.24h</td>
2084	<td>RefSeqDesign A</td>
2085	<td>Cufflinks Settings A</td>
2086	<td>Cufflinks</td>
2087	<td><i>FPKM tracking file</i>: <code>sequencing/dataset2_norm1/isoforms.fpkm_tracking</code></td>
2088	</tr>
2089	</table>
2090	<p>
2091	</li>
2092	</ol>
2093
2094	<a name="step3"></a>
2095	<h3>Third step</h3>
2096	<ol>
2097	<li>
2098	Create experiments:
2099	<table class="listing" cellspacing="0" cellpadding="2" border="0">
2100	<tr>
2101	<th>Name</th>
2102	<th>Raw data type</th>
2103	<th>Raw bioassays</th>
2104	<th>Experimental factors</th>
2105	</tr>
2106	<tr>
2107	<td>Experiment A</td>
2108	<td>GenePix</td>
2109	<td>Raw bioassay A.00h,<br>Raw bioassay A.24h,<br>Raw bioassay A.00h (dye-swap),<br>
2110	Raw bioassay A.24h (dye-swap)</td>
2111	<td>Drug resistance, Time, RIN, Dye swap, PMT gain</td>
2112	</tr>
2113	<tr>
2114	<td>Affymetrix A</td>
2115	<td>Affymetrix</td>
2116	<td>Affymetrix raw A.1,<br>Affymetrix raw A.2,<br>Affymetrix raw A.3</td>
2117	<td>Drug resistance, Time, RIN, PMT gain</td>
2118	</tr>
2119	<tr>
2120	<td>Sequence A</td>
2121	<td>Cufflinks</td>
2122	<td>SeqRaw A.00h,<br>SeqRaw A.24h</td>
2123	<td>Drug resistance, Time, RIN</td>
2124	</tr>
2125	</table>
2126	<p>
2127	</li>
2128
2129	<li><a name="inheritannotations"></a>
2130	Inherit the annotations from the scans, extracts, samples and biosource for each raw bioassay.
2131	Use the <i>auto-inherit</i> function that exists on the experiment properties
2132	tab. Make sure that all experimental factors are selected by the check boxes,
2133	then click on the <i>Auto-inherit</i> link in the column header. <br>
2134	<b>Note!</b> The <i>Dye swap</i>
2135	annotation will not get values until the next step, and the <i>Affymetrix raw A.3</i>
2136	data set is missing biomaterial parents with annotations.<br>
2137	<b>Note 2!</b> In <i>Experiment A</i> there are duplicate values for the <i>RIN</i>
2138	annotations. Fix this by manually removing the annotations that are inherited from
2139	the <i>Extract A.ref.qc</i> extract.
2140	<p>
2141
2142	</li>
2143
2144	<li>
2145	Import raw data to the Genepix and Cufflinks raw bioassays.
2146	There are two possible ways to do this:
2147	<ol>
2148	<li>Manually import to each raw bioassay.
2149	<li>Batch import to multiple raw bioassays.
2150	</ol>
2151	<p>
2152	<b>Manual import:</b> Go to the properties tab for each raw bioassay.
2153	Click on the <i>Import</i> button and use the auto-detect feature to
2154	import the raw data. Use the default configuration values except for
2155	those listed in the table below.
2156	<p>
2157
2158	<b>Batch import:</b> The batch import is started from the
2159	properties tab of the <i>experiment</i>. Click on "Import" and
2160	use the auto-detect feature with one of the files from the raw bioassays.
2161	Use the default
2162	configuration values except for those listed in the table below.
2163	The batch import should import two raw data sets in one go (since it can
2164	only work with a single file format at a time and the dye-swap files uses
2165	a different file format). Repeat the batch import a second time to import
2166	the remaining two raw data sets.
2167	<p>
2168
2169	<table class="listing" cellspacing="0" cellpadding="2" border="0">
2170	<tr>
2171	<th>Parameter</th>
2172	<th>Value</th>
2173	<th>Mode</th>
2174	</tr>
2175	<tr>
2176	<td>Feature mismatch</td>
2177	<td>smart</td>
2178	<td>both</td>
2179	</tr>
2180	<tr>
2181	<td>Invalid numeric value</td>
2182	<td>null</td>
2183	<td>both</td>
2184	</tr>
2185	<tr>
2186	<td>Log file</td>
2187	<td>~/import.log</td>
2188	<td>batch import</td>
2189	</tr>
2190	</table>
2191	<p>
2192
2193	In both cases, the import should produce the same results
2194	as in the table below. When using the batch import mode, the
2195	detailed information for each raw bioassay is only found in
2196	the log file.
2197	<table class="listing" cellspacing="0" cellpadding="2" border="0">
2198	<tr>
2199	<th>Raw bioassay</th>
2200	<th>Raw data file</th>
2201	<th>Spots inserted/with null reporter/skipped)</th>
2202	<th>Annotations created</th>
2203	</tr>
2204	<tr>
2205	<td>Raw bioassay A.00h</td>
2206	<td>genepix.mouse.v4.37k.00h.gpr</td>
2207	<td>36,864/632/768</td>
2208	<td><i>Dye swap</i>: false</td>
2209	</tr>
2210	<tr>
2211	<td>Raw bioassay A.24h</td>
2212	<td>genepix.mouse.v4.37k.24h.gpr</td>
2213	<td>36,864/632/768</td>
2214	<td><i>Dye swap</i>: false</td>
2215	</tr>
2216	<tr class="shaded">
2217	<td>Raw bioassay A.00h (dye-swap)</td>
2218	<td>genepix.mouse.v4.37k.00h.dyeswap.gpr</td>
2219	<td>36,864/632/768</td>
2220	<td><i>Dye swap</i>: true</td>
2221	</tr>
2222	<tr class="shaded">
2223	<td>Raw bioassay A.24h (dye-swap)</td>
2224	<td>genepix.mouse.v4.37k.24h.dyeswap.gpr</td>
2225	<td>36,864/632/768</td>
2226	<td><i>Dye swap</i>: true</td>
2227	</tr>
2228	<tr>
2229	<td>SeqRaw A.00h</td>
2230	<td>dataset1_norm1/isoforms.fpkm_tracking</td>
2231	<td>38,293/0/0</td>
2232	<td>-</td>
2233	</tr>
2234	<tr>
2235	<td>SeqRaw A.24h</td>
2236	<td>dataset2_norm1/isoforms.fpkm_tracking</td>
2237	<td>38,293/0/0</td>
2238	<td>-</td>
2239	</tr>
2240	</table>
2241	<p>
2242
2243	</li>
2244
2245	<li>
2246	Check the experiment overview page and use the <b>Validate</b> function
2247	for each of the three experiments.
2248	<p>
2249
2250	It should display one warning for the <b>Experiment A</b> experiment. The warning is
2251	related to a missing biosurce on the reference sample.
2252	<p>
2253	The <b>Affymetrix A</b> experiment gives some more warnings. Most of them are
2254	related to not using the project default items, missing protocols
2255	and missing hardware. There should also be an error about missing
2256	experimental factor values for the <code>Affymetrix.3</code>
2257	raw bioassay. It is expected since this comes from the reference sample
2258	which doesn't have values for those annotations. The warnings about the
2259	number of spots mismatch is expected since the array design count probesets,
2260	while the raw bioassays count probes.
2261	<p>
2262
2263	The <b>Sequence A</b> experiment also has some missing items, and a different
2264	raw data type for the experiment and raw bioassays.
2265
2266	<p>
2267	Change validation options to reduce the number of warnings:
2268	<table class="listing" cellspacing="0" cellpadding="2" border="0">
2269	<tr>
2270	<th>Validation option</th>
2271	<th>Setting</th>
2272	</tr>
2273	<tr>
2274	<td>Project defaults</td>
2275	<td>Set all to <code>Ignore</code></td>
2276	</tr>
2277	<tr>
2278	<td>Missing items</td>
2279	<td>Set all to <code>Ignore</code></td>
2280	</tr>
2281	<tr>
2282	<td>Annotations - Missing factor value</td>
2283	<td><code>Warning</code></td>
2284	</tr>
2285	<tr>
2286	<td>Other - Raw spots <> features</td>
2287	<td><code>Ignore</code></td>
2288	</tr>
2289	</table>
2290
2291	After the changes there should now only be two warnings about the
2292	missing factor values for the Affymetrix experiment and no warnings
2293	at all for the other experiments.
2294
2295	<p>
2296	</li>
2297
2298	</ol>
2299	</li>
2300	</ol>
2301
2302	<a name="analysis"></a>
2303	<h2>6. Analysis tests</h2>
2304	<p>
2305	Now it is time to analyse the data. The analysis test should be done
2306	by both a regular user and a guest.
2307	</p>
2308
2309	<ol>
2310	<li>
2311	Activate the <code>Project A</code> project<p>
2312	</li>
2313
2314	<li>
2315	Go to the <code>Experiment A</code> experiment.
2316	<p>
2317	</li>
2318
2319	<li>
2320	Clone the reporters:
2321	<table class="listing" cellspacing="0" cellpadding="2" border="0">
2322	<tr>
2323	<th>Clone template</th>
2324	<th>Clone source</th>
2325	</tr>
2326	<tr>
2327	<td>Template A</td>
2328	<td>Raw data</td>
2329	</tr>
2330	</table>
2331	Click on "Next" and wait for the plug-in to finish. It should
2332	report that 35,912 reporters has been cloned.
2333	<p>
2334	</li>
2335
2336	<li>
2337	Switch to the "Bioassay sets" tab. Create a new root bioassay set:
2338	<table class="listing" cellspacing="0" cellpadding="2" border="0">
2339	<tr>
2340	<th>Bioassay set name</th>
2341	<th>Raw bioassays</th>
2342	<th>Formula</th>
2343	</tr>
2344	<tr>
2345	<td>Root bioassay set</td>
2346	<td>all</td>
2347	<td>Mean FG - Mean BG</td>
2348	</tr>
2349	</table>
2350	Wait for the plug-in to finish.
2351	<p>
2352	</li>
2353
2354	<li>
2355	Select the created bioassay set and create a filtered bioassayset:
2356	<table class="listing" cellspacing="0" cellpadding="2" border="0">
2357	<tr>
2358	<th>Child name</th>
2359	<th>Filter preset</th>
2360	<th>Expression</th>
2361	</tr>
2362	<tr>
2363	<td>Filtered bioassay set</td>
2364	<td>-</td>
2365	<td>ch(1) > 0 && ch(2) > 0 && rep('id') != null</td>
2366	</tr>
2367	</table>
2368	Wait for the plug-in to finish. It should report that 136,498 spots remain and
2369	that 10,958 spots has been removed.
2370	<p>
2371	</li>
2372
2373	<li>
2374	Select the filtered bioassay set and run a normalization plug-in:
2375	<table class="listing" cellspacing="0" cellpadding="2" border="0">
2376	<tr>
2377	<th>Plugin</th>
2378	<th>Parameters</th>
2379	</tr>
2380	<tr>
2381	<td>Normalization: Lowess</td>
2382	<td>Accept the default parameters.</td>
2383	</tr>
2384	</table>
2385	Wait for the plug in to finish. It should report that 136,498 spots has been
2386	normalized and 0 spots has been removed.
2387	<p>
2388	</li>
2389
2390	<li>
2391	Select the normalized bioassay set and check the MA plots and
2392	the correction factor plots. Here are four examples:
2393	<table class="listing" cellspacing="0" cellpadding="2" border="0">
2394	<tr>
2395	<th>MA plots</th>
2396	<th>Correction factor plots</th>
2397	</tr>
2398	<tr>
2399	<td><img src="overview.png"><br><img src="overview.dyeswap.png"></td>
2400	<td><img src="correction.png"><br><img src="correction.dyeswap.png"></td>
2401	</tr>
2402	</table>
2403	<p>
2404	</li>
2405
2406	<li>
2407	Try the plot tool with the following plots. Use the <code>Save</code> function
2408	to save one them as a file in the BASE file system, and the <code>Download</code>
2409	function to download a plot to your computer.
2410	<table class="listing" cellspacing="0" cellpadding="2" border="0">
2411	<tr>
2412	<th>Plot type</th>
2413	<th>Y-axis preset</th>
2414	<th>X-axis preset</th>
2415	<th>Other options</th>
2416	</tr>
2417	<tr>
2418	<td>Scatter plot</td>
2419	<td>M, log2(ch1 / ch2)</td>
2420	<td>A, log10(ch1 * ch2) / 2</td>
2421	<td>-</td>
2422	</tr>
2423	<tr>
2424	<td>Histogram plot</td>
2425	<td>Count</td>
2426	<td>Ratio, ch1 / ch2</td>
2427	<td>
2428	<table border="0" cellspacing="0" cellpadding="2">
2429	<tr>
2430	<td><i>Log scale</i></td>
2431	<td>checked</td>
2432	</tr>
2433	<tr>
2434	<td><i>Bin size</i></td>
2435	<td>0.1</td>
2436	</tr>
2437	<tr>
2438	<td><i>Annotation</i></td>
2439	<td>Time</td>
2440	</tr>
2441	</table>
2442	</td>
2443	</tr>
2444	</table>
2445	<p>
2446	Here are two examples:
2447	<table class="listing" cellspacing="0" cellpadding="2" border="0">
2448	<tr>
2449	<th>Scatter plot</th>
2450	</tr>
2451	<tr>
2452	<td><img src="scatter.png"></td>
2453	</tr>
2454	</table>
2455	<p>
2456	<table class="listing" cellspacing="0" cellpadding="2" border="0">
2457	<tr>
2458	<th>Histogram plot</th>
2459	</tr>
2460	<tr>
2461	<td><img src="histogram.png"></td>
2462	</tr>
2463	</table>
2464	<p>
2465	</li>
2466
2467	</ol>
2468
2469
2470	</body>
2471	</html>

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