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Last change on this file since 3402 was 3402, checked in by Nicklas Nordborg, 16 years ago
Fixed FAQ chapters.
File size: 21.6 KB

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1	<?xml version="1.0" encoding="UTF-8"?>
2	<!DOCTYPE part PUBLIC
3	"-//Dawid Weiss//DTD DocBook V3.1-Based Extension for XML and graphics inclusion//EN"
4	"../../../../lib/docbook/preprocess/dweiss-docbook-extensions.dtd">
5	<!--
6	$Id: faqs.xml 3246 2007-04-16 14:12:23Z martin $
7
8	Copyright (C) Authors contributing to this file.
9
10	This file is part of BASE - BioArray Software Environment.
11	Available at http://base.thep.lu.se/
12
13	BASE is free software; you can redistribute it and/or
14	modify it under the terms of the GNU General Public License
15	as published by the Free Software Foundation; either version 2
16	of the License, or (at your option) any later version.
17
18	BASE is distributed in the hope that it will be useful,
19	but WITHOUT ANY WARRANTY; without even the implied warranty of
20	MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
21	GNU General Public License for more details.
22
23	You should have received a copy of the GNU General Public License
24	along with this program; if not, write to the Free Software
25	Foundation, Inc., 59 Temple Place - Suite 330,
26	Boston, MA 02111-1307, USA.
27	-->
28
29	<part id="faqs">
30	<?dbhtml dir="faqs"?>
31	<title>Frequently Asked Questions</title>
32
33	<chapter id="faqs.reporter">
34	<title>Reporters related FAQs</title>
35	<qandaset defaultlabel='qanda'>
36	<?dbhtml cellspacing="0px" cellpadding="0px" ?>
37	<qandaentry>
38	<question>
39	<simpara>
40	I can't find my favourite database for annotating reporters. Can I add
41	my database to BASE2 and if so, How should it proceed?
42	</simpara>
43	</question>
44	<answer>
45	<simpara>
46	Yes, you can add resources to annotate reporters. You will need to
47	upgrade BASE2 and you may have to contact your system administrator for
48	doing so.
49	</simpara>
50
51	<simpara>
52	In order to change, remove or add annotation fields attached to
53	reporters, you will need modify the <filename>extended-properties.xml</filename>
54	file and run a BASE update. Please refer to section
55	<xref linkend="installation_upgrade.installation" />
56	for information about both processes. Once done with the upgrade, you'll
57	have to defined a new reporter import plug-in. Instructions can be found
58	in <xref linkend="plugins" />.
59	</simpara>
60	</answer>
61	</qandaentry>
62
63	<qandaentry>
64	<question>
65	<simpara>
66	I have made a mistake while loading my reporters. How can I delete them
67	all in one go ?
68	</simpara>
69	</question>
70	<answer>
71	<simpara>
72	Please contact your system administrator. This is not possible
73	to do from the web interface. The administrator has to do this
74	manually by executing SQL from the database prompt.
75	</simpara>
76	</answer>
77	</qandaentry>
78	</qandaset>
79	</chapter>
80
81	<chapter id="faqs.arraydesign">
82	<title>Array design related FAQs</title>
83	<qandaset defaultlabel='qanda'>
84	<?dbhtml cellspacing="0px" cellpadding="0px" ?>
85	<qandaentry>
86	<question>
87	<para>
88	What it the best way to create an array design in BASE2 when starting
89	from a GAL file?
90	</para>
91	</question>
92	<answer>
93	<para>
94	This requires some work but here is the
95	procedure to remember:
96	</para>
97	<para>
98	A gal file tells where <guilabel>Reporters</guilabel>
99	have been spotted on an array. So a GAL file can be used to do 2 things
100	</para>
101	<orderedlist>
102	<listitem>
103	<para>
104	Define the features of an array design for a non-Affy platform
105	using the <guilabel>Reporter Map importer plug-in</guilabel>.
106	</para>
107	<para>
108	To do so, after having created an new array design, go to the
109	single-item view by of the newly created array design.
110	Click on the &gbImport;
111	the button. If you don't see it, it means that you have not
112	enough privileges (contact the administrator).
113	</para>
114	<para>
115	This starts the plug-in configuration wizard. Select
116	the <guilabel>auto detect</guilabel> option and in the
117	next step your GAL file.
118	</para>
119	<para>
120	Now, there is the risk that no file format has been defined
121	for GAL files. This must be done by an administrator or other user
122	with proper privileges. See <xref linkend="plugins.configuration" />
123	for infomation about this.
124	</para>
125	<para>
126	Once done (and if everything went fine), you can see from the
127	Array Design list view that the
128	<guilabel>Has features</guilabel>
129	entry has been modified and is set to 'Yes (n)' where n
130	indicates the number of spots (features) for this array.
131	</para>
132	<note>
133	<para>
134	Features can also be loaded from a Genepix GPR file
135	with the same procedure.
136	</para>
137	</note>
138	</listitem>
139	<listitem>
140	<para>
141	Define the
142	<guilabel>Reporters</guilabel>
143	present on the array design using the
144	<guilabel>Reporter importer plug-in</guilabel>.
145	</para>
146	<para>
147	To do so, Go to
148	<menuchoice>
149	<guimenu>View</guimenu>
150	<guimenuitem>Reporters</guimenuitem>
151	</menuchoice>
152	and click on
153	&gbImport;. This starts a
154	<guilabel>Reporter Importer plug-in</guilabel>
155	</para>
156	<para>
157	More information about importing Reporters can be found in
158	<xref linkend="reporters" />
159	</para>
160	</listitem>
161	</orderedlist>
162	</answer>
163	</qandaentry>
164
165	<qandaentry>
166	<question>
167	<para>
168	I am confused. What is the difference between
169	<guilabel>Reporter map importer</guilabel>,
170	<guilabel>Print map importer</guilabel> and
171	<guilabel>Reporter importer</guilabel>?
172	</para>
173	</question>
174	<answer>
175	<para>
176	The reporter map and print map importer are used to
177	import features to an array design.
178	The latter one must be used when your array design is connected to PCR
179	plates and supports two file formats: Biorobotics TAM
180	and Molecularware MWBR. See
181	<ulink url="http://www.flychip.org.uk/protocols/robotic_spotting/fileformats.php"
182	>http://www.flychip.org.uk/protocols/robotic_spotting/fileformats.php</ulink>
183	for more information about those file formats.
184	If you are only using commercial platforms or if you don't use plates in the array lims, you
185	have no need for the print map importer and should use the reporter
186	map importer instead.
187	</para>
188
189	<para>
190	The reporter importer is used to load reporter annotations into BASE.
191	</para>
192	</answer>
193	</qandaentry>
194	</qandaset>
195	</chapter>
196
197	<chapter id="faqs.biomaterial">
198	<title>Biomaterial, Protocol, Hardware, Software related FAQS</title>
199	<qandaset defaultlabel='qanda'>
200	<?dbhtml cellspacing="0px" cellpadding="0px" ?>
201	<qandaentry>
202	<question>
203	<para>
204	I have just created a new item but I can not see
205	it. Am I doing something wrong?
206	</para>
207	</question>
208	<answer>
209	<para>
210	Try clearing the filter. To do so: use the
211	<guilabel>view / presets</guilabel>
212	dropdown and select the
213	<guilabel>clear filter</guilabel>
214	entry. This will remove all characters in the search boxes and all
215	preselection of item in the drop down lists. If this does not solve your
216	problem, then check if the <guilabel>view / presets</guilabel>
217	has the <guilabel>owned by me</guilabel> entry selected.
218	</para>
219	</answer>
220	</qandaentry>
221
222	<qandaentry>
223	<question>
224	<para>
225	I can only see XX columns in the list view but I know I have
226	a lot more information. Is there a way I can customize the column
227	display?
228	</para>
229	</question>
230	<answer>
231	<para>
232	Yes, you can display many more columns. See <xref
233	linkend="webclient.itemlist.columns" />.
234	</para>
235	</answer>
236	</qandaentry>
237
238	<qandaentry>
239	<question>
240	<para>
241	Is it possible to sort the values in a column in the list view?
242	</para>
243	</question>
244	<answer>
245	<para>
246	Of course it is. See <xref linkend="webclient.itemlist.order" />.
247	</para>
248	</answer>
249	</qandaentry>
250
251	<qandaentry>
252	<question>
253	<para>
254	Is it possible to sort the annotation types from
255	<guilabel>Annotation & parameters</guilabel> tab in the
256	single-item view?
257	</para>
258	</question>
259	<answer>
260	<para>
261	No. This is not possible at the moment. The annotations are always sorted
262	by the name of the annotation type.
263	</para>
264	</answer>
265	</qandaentry>
266
267	<qandaentry>
268	<question>
269	<para>
270	I have to create pools of samples in my experiment due to scarcity of
271	the biological material. Can I represent those pooled samples is BASE2?
272	</para>
273	</question>
274	<answer>
275	<para>
276	Yes, you can. From the sample list select a number of samples
277	by marking their checkboxes. Then click on the <guibutton>Pool</guibutton>
278	button. For more information see
279	<xref linkend="sample.manage.createsample.pool" />.
280	Pooling can also be applied to extracts and labeled extracts.
281	</para>
282	</answer>
283	</qandaentry>
284	<qandaentry>
285	<question>
286	<para>
287	I would like to add a software type in BASE2 but there is no button for
288	doing so. Is it possible?
289	</para>
290	</question>
291	<answer>
292	<para>
293	No, this is not possible, since there is only one place
294	software is used, namely to register the feature extraction
295	of a scanned image.
296	</para>
297	</answer>
298	</qandaentry>
299
300	<qandaentry>
301	<question>
302	<para>
303	I need to create a new hardware type but the
304	&gbNew;
305	button is grey and does not work. Why?
306	</para>
307	</question>
308	<answer>
309	<para>
310	Your privileges are not high enough and you have not been granted
311	permission to create hardware types. Contact your BASE2 administrator.
312	For more information about permissions, please refer to
313	<xref linkend="user_administration" />.
314	</para>
315	</answer>
316	</qandaentry>
317	<qandaentry>
318	<question>
319	<para>
320	I have created an Annotation Type <userinput>Temperature</userinput>
321	and shared it to everyone but when I want to use it for annotating a
322	sample, I can not find it! How is that?
323	</para>
324	</question>
325	<answer>
326	<para>
327	The most likely explanation is that this particular annotation
328	type has been declared as a protocol parameter. This means that it will
329	only be displayed in BASE2 if you have used a sample creation protocol
330	which uses that parameter.
331	</para>
332	</answer>
333	</qandaentry>
334
335	<qandaentry>
336	<question>
337	<para>
338	I have carried out an experiment using both Affymetrix and Agilent
339	arrays but I can not select more than one raw data type in BASE2. What
340	should I do?
341	</para>
342	</question>
343	<answer>
344	<para>
345	In this particular case and because you are using 2 different raw data
346	file formats, you will have to split your experiment in 2. One
347	experiment for those samples processed using Affymetrix platform and
348	another one using Agilent platform. You don't necessarily have to
349	provide all information about the samples again but simply create new
350	raw bioassay data which can be grouped in a new experiment.
351	</para>
352	</answer>
353	</qandaentry>
354	</qandaset>
355	</chapter>
356
357	<chapter id="faqs.datafiles_rawdata">
358	<title>Data Files and Raw Data related FAQs</title>
359	<qandaset defaultlabel='qanda'>
360	<?dbhtml cellspacing="0px" cellpadding="0px" ?>
361	<qandaentry>
362	<question>
363	<para>
364	It seems that BASE2 does not support the datafiles generated by my brand
365	new scanner. Is it possible to add it to BASE2?
366	</para>
367	</question>
368	<answer>
369	<para>
370	Yes it is possible to extend BASE2 so that it can support your system.
371	You will need to define a new raw data type for BASE2 by modifying
372	the <filename>raw-datatypes.xml</filename> configuration file.
373	</para>
374	<para>
375	Then, you will have to run the <filename>updatedb.sh</filename>
376	to make the new raw data type available to the system. See
377	<xref linkend="installation_upgrade.upgrade" />.
378	</para>
379	<para>
380	Finally, you will have to configure a raw data import plug-in in order to
381	be able to create rawbioassays. See
382	<xref linkend="plugins.configuration" />
383	and
384	<xref linkend="experiments_analysis.rawbioassay.rawdata" />
385	for further information.
386	</para>
387	</answer>
388	</qandaentry>
389
390	<qandaentry>
391	<question>
392	<para>
393	I have created a raw bioassay which is not Affy but the system does not
394	allow me to upload a datafile whereas it is possible to do so if I
395	declared my rawbioassay of type Affy. Why?
396	</para>
397	</question>
398	<answer>
399	<para>
400	This is normal. BASE2 deals with Affymetrix datafiles differently. BASE2
401	stores native Affymetrix file and does not load the value in tables as
402	it does for other platforms. See <xref linkend="experiments_analysis.rawbioassay.rawdata" />
403	for more information.
404	</para>
405	</answer>
406	</qandaentry>
407
408	<qandaentry>
409	<question>
410	<para>
411	I have created a raw bioassay using Affymetrix CEL file but the
412	interface says 'no spot'. I have really loaded the file! Why?
413	</para>
414	</question>
415	<answer>
416	<para>
417	Again, this is because of the specific treatement of
418	Affymetrix files compared to other platforms. Affymetrix data
419	is kept in the files and are not imported into the database.
420	Currently, the number of spots can only be counted when
421	data is located in the database.
422	</para>
423	</answer>
424	</qandaentry>
425
426	<qandaentry>
427	<question>
428	<para>Are Affymetrix CDT and CAB files supported by BASE2?</para>
429	</question>
430	<answer>
431	<para>
432	There is no support for CDT or CAB. Currently only CDF and CEL files are
433	supported by the Affymetrix plug-ins. Annotation files (.csv) are used
434	for uploading probeset (reporter in BASE language) information. The
435	issue of supporting CDT and CAB files is an import and a plug-in issue.
436	There are two ways to solve this:
437	<orderedlist>
438	<listitem>
439	<para>
440	Write code that treats the files in a proper way and submit
441	the solution to the developer team (preferred route).
442	</para>
443	</listitem>
444	<listitem>
445	<para>
446	Submit a ticket through
447	<ulink url="http://base.thep.lu.se">http://base.thep.lu.se</ulink>
448	explaining what you'd like to see with respect to to CDT and CAB files.
449	</para>
450	</listitem>
451	</orderedlist>
452
453	<note>
454	<para>
455	To include CDT and CAB support to BASE, the file formats must be
456	open, that is we must be able to read them without proprietary
457	non-distributable code.
458	</para>
459	</note>
460	</para>
461	</answer>
462	</qandaentry>
463
464	<qandaentry>
465	<question>
466	<para>Are Illumina datafiles supported by BASE2 ?</para>
467	</question>
468	<answer>
469	<para>
470	Not by default, but the BASE user community has provided
471	a workaround to make it possible.
472	See
473	<ulink url="http://base.thep.lu.se/ticket/486">ticket 486</ulink>
474	on the BASE website for more information.
475	</para>
476	</answer>
477	</qandaentry>
478	</qandaset>
479	</chapter>
480
481	<chapter id="faqs.data_repositories">
482	<title>Data Deposition to Public Repositories related FAQs</title>
483	<qandaset defaultlabel='qanda'>
484	<?dbhtml cellspacing="0px" cellpadding="0px" ?>
485	<qandaentry>
486	<question>
487	<para>
488	I am asked by reviewers to deposit my microarray data in a public
489	repository. How can BASE2 help me?
490	</para>
491	</question>
492	<answer>
493	<para>
494	The BASE2 development team are working on a plug-in
495	that produces a Tab2Mage file accepted by ArrayExpress.
496	For the plug-in to work properly, a series of rules need to be
497	followed, please refer to
498	<xref linkend="experiments_analysis.magexport" />
499	for additional information.
500	</para>
501	<para>
502	More information about the Tab2Mage format can be found at
503	<ulink url="http://tab2mage.sourceforge.net"
504	>http://tab2mage.sourceforge.net</ulink>.
505	To send the submission to array express, use the ArrayExpress FTP site
506	at <ulink url="ftp://ftp.ebi.ac.uk pwd">ftp://ftp.ebi.ac.uk pwd</ulink>.
507	Login with username and password <userinput>aexpress</userinput>.
508	</para>
509	<warning>
510	<para>
511	The current export plug-in does not support Tab2Mage normalized and
512	transformed files, so some additional work might be required to be
513	fully complient, please refer to Tab2Mage helpnotes for creating
514	these final gene expression files and update the Tab2Mage files.
515	</para>
516	</warning>
517	</answer>
518	</qandaentry>
519
520	<qandaentry>
521	<question>
522	<para>
523	Repositories want me to be MIAME compliant but how do I know that?
524	</para>
525	</question>
526	<answer>
527	<itemizedlist>
528	<listitem>
529	<para>
530	Make sure to format your annotation types following the rules
531	detailed in <xref linkend="experiments_analysis.magexport" />.
532	</para>
533	</listitem>
534	<listitem>
535	<para>
536	Before exporting, it is probably a good idea to run the
537	<guilabel>Experiment Overview</guilabel>
538	detailed in
539	<xref linkend="experiments_analysis.experiment.overview" />.
540	By selecting stringent criteria from the interface, the tool will
541	detect all missing information that could be requested by
542	repositories.
543	</para>
544	</listitem>
545	<listitem>
546	<para>
547	If the experiment overview does not report any error any more,
548	you can run the Tab2Mage export plug-in suitable for ArrayExpress.
549	</para>
550	</listitem>
551	</itemizedlist>
552	</answer>
553	</qandaentry>
554
555	<qandaentry>
556	<question>
557	<para>
558	I have exported in Tab2Mage file, does it mean I am MIAME compliant?
559	</para>
560	</question>
561	<answer>
562	<para>
563	No, not necessarily! Tab2Mage exporter complies with Tab2Mage
564	specifications so you will be Tab2Mage compliant. However, MIAME
565	compliance depends very much on the kind of annotation you have
566	supplied. Please refer to the previous question for more information
567	about how to check for MIAME compliance in BASE2 using the Experiment
568	overview function.
569	</para>
570	</answer>
571	</qandaentry>
572
573	<qandaentry>
574	<question>
575	<para>
576	I have deleted the datafiles from BASE2 file systems since I have
577	imported them in tables. So I don't have datafiles to send to
578	ArrayExpress anymore.
579	</para>
580	</question>
581	<answer>
582	<para>
583	You can export the data from the tables again. Go to the
584	<guilabel>Raw data</guilabel> tab for each of the
585	raw bioassays you need to export. Use the
586	&gbExport; button to export the data. See
587	<xref linkend="import_export_data.export.table_export" />.
588	for more information.
589	</para>
590	</answer>
591	</qandaentry>
592
593	<qandaentry>
594	<question>
595	<para>
596	I have created pooled samples in BASE2. Can I export in Tab2Mage format?
597	</para>
598	</question>
599	<answer>
600	<para>
601	No, sorry, not for the moment. The
602	Tab2Mage exporter does not support pooling events. We are working on
603	adding this features in future version of the plug-in.
604	</para>
605	</answer>
606	</qandaentry>
607	</qandaset>
608	</chapter>
609
610	<chapter id="faqs.analysis">
611	<title>Analysis related FAQs</title>
612	<qandaset defaultlabel='qanda'>
613	<?dbhtml cellspacing="0px" cellpadding="0px" ?>
614	<qandaentry>
615	<question>
616	<para>
617	Is it possible to use the formula filter to filter for
618	<constant>null</constant>
619	values (or non-<constant>null</constant> values)?
620	</para>
621	</question>
622	<answer>
623	<para>
624	It is possible to trick the system to filter out <constant>null</constant>
625	values but not non-<constant>null</constant> values. Use an expression like:
626	<userinput>ch(1) == 0 \|\| ch(1) != 0</userinput>. This will match
627	all values, except <constant>null</constant> vaues.
628	</para>
629	</answer>
630	</qandaentry>
631
632	<qandaentry>
633	<question>
634	<para>
635	OK, I have uploaded 40 CEL files in BASE2 but are there any tool to
636	perform normalization on Affymetrix raw data?
637	</para>
638	</question>
639	<answer>
640	<para>
641	Yes, there is. BASE2 team has created a plug-in based on
642	<ulink url="http://rmaexpress.bmbolstad.com/">
643	RMAExpress methods from Bolstad and Irizarry</ulink> so you can normalize
644	Affymetrix datasets of reasonable size (not 1000 CEL files at a time
645	though even though this might depend on your set-up...)
646	The plug-in is not included in a standard BASE installation, but
647	can be downloaded from the <ulink url="http://lev.thep.lu.se/trac/baseplugins"
648	>BASE plug-ins web site</ulink>.
649	</para>
650	</answer>
651	</qandaentry>
652	</qandaset>
653	</chapter>
654	</part>

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