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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) 2007 Peter Johansson, Nicklas Nordborg, Philippe Rocca-Serra, Martin Svensson
9	Copyright (C) 2008 Jari Hakkinen, Nicklas Nordborg
10
11	This file is part of BASE - BioArray Software Environment.
12	Available at http://base.thep.lu.se/
13
14	BASE is free software; you can redistribute it and/or
15	modify it under the terms of the GNU General Public License
16	as published by the Free Software Foundation; either version 3
17	of the License, or (at your option) any later version.
18
19	BASE is distributed in the hope that it will be useful,
20	but WITHOUT ANY WARRANTY; without even the implied warranty of
21	MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
22	GNU General Public License for more details.
23
24	You should have received a copy of the GNU General Public License
25	along with this program; if not, write to the Free Software
26	Foundation, Inc., 59 Temple Place - Suite 330,
27	Boston, MA 02111-1307, USA.
28	-->
29
30	<part id="faqsdoc">
31	<?dbhtml dir="faqsdoc"?>
32	<title>FAQ</title>
33
34	<chapter id="faqs" chunked="0">
35	<?dbhtml dir="faqs"?>
36	<title>Frequently Asked Questions with answers</title>
37
38	<para>
39	This chapter presents a list of solutions to common problems and
40	tasks in BASE. The information is is collected from the mailing
41	lists, private communication, and from issues frequently
42	encountered in BASE introduction courses. If you have BASE
43	solutions that should be added to this chapter please contact us
44	through the usual communication channels, see
45	<xref linkend="resources" /> for contact information.
46	</para>
47
48	<sect1 id="faqs.reporter">
49	<title>Reporter related questions with answers</title>
50	<qandaset defaultlabel='qanda'>
51	<?dbhtml cellspacing="0px" cellpadding="0px" ?>
52
53	<qandaentry>
54	<question>
55	<simpara>
56	My favourite database is not used for annotating reporters. Can I add
57	my database to BASE and if so, how should it proceed?
58	</simpara>
59	</question>
60	<answer>
61	<simpara>
62	Yes, you can add resources to annotate reporters. You will need to
63	upgrade BASE and you may have to contact your system administrator for
64	doing so.
65	</simpara>
66
67	<simpara>
68	In order to change, remove or add annotation fields attached to
69	reporters, you will need modify the <filename>extended-properties.xml</filename>
70	file and run a BASE update. Please refer to section
71	<xref linkend="installation_upgrade.installation" />
72	for information about both processes. Once done with the upgrade, you'll
73	have to define a new reporter import plug-in. Instructions can be found
74	in <xref linkend="plugins" />.
75	</simpara>
76	</answer>
77	</qandaentry>
78
79	<qandaentry>
80	<question>
81	<simpara>
82	I have made a mistake while loading my reporters. How can I delete them
83	all in one go ?
84	</simpara>
85	</question>
86	<answer>
87	<simpara>
88	The reporter import plug-in can be executed in <emphasis>delete</emphasis>
89	mode. Run the plug-in again and select the same file you just for the import.
90	Select the <guilabel>Mode=delete</guilabel> option.
91	In the <guilabel>Error handling</guilabel> section select the
92	<guilabel>Reporter is used=skip</guilabel> option. This will delete all
93	reporters that was created in the previous import.
94	</simpara>
95	</answer>
96	</qandaentry>
97
98	<qandaentry>
99	<question>
100	<simpara>
101	I get a message "Error: Unable to import root
102	bioassay. Item not found:
103	Reporter[externalId=AFFX-2315060]" when i try to create
104	a root bioassayset.
105	</simpara>
106	</question>
107	<answer>
108	<simpara>
109	BASE requires all reporters (probesets in Affymetrix
110	speak) to be stored in the database before they can be
111	used. The reporter information is typically imported
112	from a reporter annotation file but in some cases the
113	reporter annotation file supplied by Affymetrix fails to
114	describe all reporters (probesets) on a chip. BASE will
115	refuse to store data related to such chips until the
116	missing reporters are added to the database. Hence the
117	rejection of the new root bioassayset.
118	</simpara>
119
120	<simpara>
121	The resolution is straightforward, simply import the
122	probeset information from the CDF file associated with
123	the array design. The catch is that normal BASE user
124	credential is not enough to perform the import therefore
125	someone with proper credential (the BASE server
126	administrator is one of them) must perform the
127	import. Follow the instructions at
128	<xref linkend="reporters.import" /> to import
129	reporters. Make sure to select plug-in option to ignore
130	already existing reporters when starting the import
131	otherwise the existing reporter annotations will be
132	changed. The goal here is to add missing reporters to
133	allow BASE work with your data. The CDF file does not
134	contain any annotation information and cannot be used to
135	annotate reporters.
136	</simpara>
137	</answer>
138	</qandaentry>
139
140	</qandaset>
141	</sect1>
142
143	<sect1 id="faqs.arraydesign">
144	<title>Array design related questions with answers</title>
145	<qandaset defaultlabel='qanda'>
146	<?dbhtml cellspacing="0px" cellpadding="0px" ?>
147	<qandaentry>
148	<question>
149	<para>
150	What it the best way to create an array design in BASE2 when starting
151	from a GAL file?
152	</para>
153	</question>
154	<answer>
155	<para>
156	This requires some work but here is the
157	procedure to remember:
158	</para>
159	<para>
160	A gal file tells where <guilabel>Reporters</guilabel>
161	have been spotted on an array. So a GAL file can be used to do 2 things
162	</para>
163	<orderedlist>
164	<listitem>
165	<para>
166	Define the features of an array design for a non-Affymetrix platform
167	using the <guilabel>Reporter Map importer plug-in</guilabel>.
168	</para>
169	<para>
170	To do so, after having created an new array design, go to the
171	single-item view by of the newly created array design.
172	Click on the &gbImport;
173	the button. If you do not see it, it means that you have not
174	enough privileges (contact the administrator).
175	</para>
176	<para>
177	This starts the plug-in configuration wizard. Select
178	the <guilabel>auto detect</guilabel> option and in the
179	next step your GAL file.
180	</para>
181	<para>
182	Now, there is the risk that no file format has been defined
183	for GAL files. This must be done by an administrator or other user
184	with proper privileges. See <xref linkend="plugins.configuration" />
185	for information about this.
186	</para>
187	<para>
188	Once done (and if everything went fine), you can see from the
189	Array Design list view that the
190	<guilabel>Has features</guilabel>
191	entry has been modified and is set to 'Yes (n)' where n
192	indicates the number of spots (features) for this array.
193	</para>
194	<note>
195	<para>
196	Features can also be loaded from a Genepix GPR file
197	with the same procedure.
198	</para>
199	</note>
200	</listitem>
201	<listitem>
202	<para>
203	Define the
204	<guilabel>Reporters</guilabel>
205	present on the array design using the
206	<guilabel>Reporter importer plug-in</guilabel>.
207	</para>
208	<para>
209	To do so, Go to
210	<menuchoice>
211	<guimenu>View</guimenu>
212	<guimenuitem>Reporters</guimenuitem>
213	</menuchoice>
214	and click on
215	&gbImport;. This starts a
216	<guilabel>Reporter Importer plug-in</guilabel>
217	</para>
218	<para>
219	More information about importing Reporters can be found in
220	<xref linkend="reporters" />
221	</para>
222	</listitem>
223	</orderedlist>
224	</answer>
225	</qandaentry>
226
227	<qandaentry>
228	<question>
229	<para>
230	I am confused. What is the difference between
231	<guilabel>Reporter map importer</guilabel>,
232	<guilabel>Print map importer</guilabel> and
233	<guilabel>Reporter importer</guilabel>?
234	</para>
235	</question>
236	<answer>
237	<para>
238	The reporter map and print map importer are used to
239	import features to an array design.
240	The latter one must be used when your array design is connected to PCR
241	plates and supports two file formats: Biorobotics TAM
242	and Molecularware MWBR. See
243	<ulink url="http://www.flychip.org.uk/protocols/robotic_spotting/fileformats.php"
244	>http://www.flychip.org.uk/protocols/robotic_spotting/fileformats.php</ulink>
245	for more information about those file formats.
246	If you are only using commercial platforms or if you do not use plates in the array LIMS, you
247	have no need for the print map importer and should use the reporter
248	map importer instead.
249	</para>
250
251	<para>
252	The reporter importer is used to load reporter annotations into BASE.
253	</para>
254	</answer>
255	</qandaentry>
256	</qandaset>
257	</sect1>
258
259	<sect1 id="faqs.biomaterial">
260	<title>Biomaterial, Protocol, Hardware, Software related questions with answers</title>
261	<qandaset defaultlabel='qanda'>
262	<?dbhtml cellspacing="0px" cellpadding="0px" ?>
263	<qandaentry>
264	<question>
265	<para>
266	I have just created a new item but I can not see
267	it. Am I doing something wrong?
268	</para>
269	</question>
270	<answer>
271	<para>
272	Try clearing the filter. To do so: use the
273	<guilabel>view / presets</guilabel>
274	dropdown and select the
275	<guilabel>clear filter</guilabel>
276	entry. This will remove all characters in the search boxes and all
277	preselection of item in the drop down lists. If this does not solve your
278	problem, then check if the <guilabel>view / presets</guilabel>
279	has the <guilabel>owned by me</guilabel> entry selected.
280	</para>
281	</answer>
282	</qandaentry>
283
284	<qandaentry>
285	<question>
286	<para>
287	I can only see XX columns in the list view but I know I have
288	a lot more information. Is there a way I can customise the column
289	display?
290	</para>
291	</question>
292	<answer>
293	<para>
294	Yes, you can display many more columns. See <xref
295	linkend="webclient.itemlist.columns" />.
296	</para>
297	</answer>
298	</qandaentry>
299
300	<qandaentry>
301	<question>
302	<para>
303	Is it possible to sort the values in a column in the list view?
304	</para>
305	</question>
306	<answer>
307	<para>
308	Of course it is. See <xref linkend="webclient.itemlist.order" />.
309	</para>
310	</answer>
311	</qandaentry>
312
313	<qandaentry>
314	<question>
315	<para>
316	Is it possible to sort the annotation types from
317	<guilabel>Annotation & parameters</guilabel> tab in the
318	single-item view?
319	</para>
320	</question>
321	<answer>
322	<para>
323	No. This is not possible at the moment. The annotations are always sorted
324	by the name of the annotation type.
325	</para>
326	</answer>
327	</qandaentry>
328
329	<qandaentry>
330	<question>
331	<para>
332	I have to create pools of samples in my experiment due to scarcity of
333	the biological material. Can I represent those pooled samples is BASE2?
334	</para>
335	</question>
336	<answer>
337	<para>
338	Yes, you can. From the sample list select a number of samples
339	by marking their checkboxes. Then click on the <guibutton>Pool</guibutton>
340	button. For more information see
341	<xref linkend="biomaterials.samples.create" />.
342	Pooling can also be applied to extracts and labeled extracts.
343	</para>
344	</answer>
345	</qandaentry>
346	<qandaentry>
347	<question>
348	<para>
349	I would like to add a software type in BASE2 but there is no button for
350	doing so. Is it possible?
351	</para>
352	</question>
353	<answer>
354	<para>
355	No, this is not possible, since there is only one place
356	software is used, namely to register the feature extraction
357	of a scanned image.
358	</para>
359	</answer>
360	</qandaentry>
361
362	<qandaentry>
363	<question>
364	<para>
365	I need to create a new hardware type but the
366	&gbNew;
367	button is grey and does not work. Why?
368	</para>
369	</question>
370	<answer>
371	<para>
372	Your privileges are not high enough and you have not been granted
373	permission to create hardware types. Contact your BASE2 administrator.
374	For more information about permissions, please refer to
375	<xref linkend="user_administration" />.
376	</para>
377	</answer>
378	</qandaentry>
379	<qandaentry>
380	<question>
381	<para>
382	I have created an Annotation Type <userinput>Temperature</userinput>
383	and shared it to everyone but when I want to use it for annotating a
384	sample, I can not find it! How is that?
385	</para>
386	</question>
387	<answer>
388	<para>
389	The most likely explanation is that this particular annotation
390	type has been declared as a protocol parameter. This means that it will
391	only be displayed in BASE2 if you have used a sample creation protocol
392	which uses that parameter.
393	</para>
394	</answer>
395	</qandaentry>
396
397	<qandaentry>
398	<question>
399	<para>
400	I have carried out an experiment using both Affymetrix and Agilent
401	arrays but I can not select more than one raw data type in BASE2. What
402	should I do?
403	</para>
404	</question>
405	<answer>
406	<para>
407	In this particular case and because you are using 2 different raw data
408	file formats, you will have to split your experiment in 2. One
409	experiment for those samples processed using Affymetrix platform and
410	another one using Agilent platform. You do not necessarily have to
411	provide all information about the samples again but simply create new
412	raw bioassay data which can be grouped in a new experiment.
413	</para>
414	</answer>
415	</qandaentry>
416	</qandaset>
417	</sect1>
418
419	<sect1 id="faqs.datafiles_rawdata">
420	<title>Data Files and Raw Data related questions with answers</title>
421	<qandaset defaultlabel='qanda'>
422	<?dbhtml cellspacing="0px" cellpadding="0px" ?>
423	<qandaentry>
424	<question>
425	<para>
426	It seems that BASE2 does not support the data files generated by my brand
427	new scanner. Is it possible to add it to BASE2?
428	</para>
429	</question>
430	<answer>
431	<para>
432	Yes it is possible to extend BASE2 so that it can support your system.
433	You will need to define a new raw data type for BASE2 by modifying
434	the <filename>raw-datatypes.xml</filename> configuration file.
435	</para>
436	<para>
437	Then, you will have to run the <filename>updatedb.sh</filename>
438	to make the new raw data type available to the system. See
439	<xref linkend="installation_upgrade.upgrade" />.
440	</para>
441	<para>
442	Finally, you will have to configure a raw data import plug-in in order to
443	be able to create rawbioassays. See
444	<xref linkend="plugins.configuration" />
445	and
446	<xref linkend="experiments_analysis.rawbioassay.rawdata" />
447	for further information.
448	</para>
449	</answer>
450	</qandaentry>
451
452	<qandaentry>
453	<question>
454	<para>
455	I have created a raw bioassay which is not Affymetrix but the system does not
456	allow me to upload a data file whereas it is possible to do so if I
457	declared my rawbioassay of type Affymetrix. Why?
458	</para>
459	</question>
460	<answer>
461	<para>
462	This is normal. BASE2 deals with Affymetrix data files differently. BASE2
463	stores native Affymetrix file and does not load the value in tables as
464	it does for other platforms. See <xref linkend="experiments_analysis.rawbioassay.rawdata" />
465	for more information.
466	</para>
467	</answer>
468	</qandaentry>
469
470	<qandaentry>
471	<question>
472	<para>
473	I have created a raw bioassay using Affymetrix CEL file but the
474	interface says 'no spot'. I have really loaded the file! Why?
475	</para>
476	</question>
477	<answer>
478	<para>
479	Again, this is because of the specific treatment of
480	Affymetrix files compared to other platforms. Affymetrix data
481	is kept in the files and are not imported into the database.
482	Currently, the number of spots can only be counted when
483	data is located in the database.
484	</para>
485	</answer>
486	</qandaentry>
487
488	<qandaentry>
489	<question>
490	<para>Are Affymetrix CDT and CAB files supported by BASE2?</para>
491	</question>
492	<answer>
493	<para>
494	There is no support for CDT or CAB. Currently only CDF and CEL files are
495	supported by the Affymetrix plug-ins. Annotation files (.csv) are used
496	for uploading probeset (reporter in BASE language) information. The
497	issue of supporting CDT and CAB files is an import and a plug-in issue.
498	There are two ways to solve this:
499	<orderedlist>
500	<listitem>
501	<para>
502	Write code that treats the files in a proper way and submit
503	the solution to the developer team (preferred route).
504	</para>
505	</listitem>
506	<listitem>
507	<para>
508	Submit a ticket through
509	<ulink url="http://base.thep.lu.se">http://base.thep.lu.se</ulink>
510	explaining what you'd like to see with respect to to CDT and CAB files.
511	</para>
512	</listitem>
513	</orderedlist>
514
515	<note>
516	<para>
517	To include CDT and CAB support to BASE, the file formats must be
518	open, that is we must be able to read them without proprietary
519	non-distributable code.
520	</para>
521	</note>
522	</para>
523	</answer>
524	</qandaentry>
525
526	<qandaentry>
527	<question>
528	<para>Are Illumina data files supported by BASE2 ?</para>
529	</question>
530	<answer>
531	<para>
532	Yes, but not by default. There is
533	an <ulink url="http://baseplugins.thep.lu.se/wiki/net.sf.basedb.illumina">Illumina
534	package</ulink> that provides Illumina support to
535	BASE. The package is straightforward to install, visit
536	the package site for more information.
537	</para>
538	</answer>
539	</qandaentry>
540
541	<qandaentry>
542	<question>
543	<para>Unzipped files never inherit file type specified
544	during upload, why?</para>
545	</question>
546	<answer>
547	<para>
548	Unfortunately this is an "unfixable" defect. The API for
549	unpacking files is a kind of plug-in interface
550	(FileUnpacker) that has been made public. The "mistake"
551	is that the API does not include any information from
552	the file upload dialog except the directory to upload to
553	(not even the file name is included). Introducing new
554	method or parameters will break the API and we prefer to
555	not do that.
556	</para>
557	<para>
558	As a workaround to this problem the extension of each
559	file is checked against the list of MIME types
560	(<menuchoice>
561	<guimenu>Administrate</guimenu>
562	<guimenuitem>Types</guimenuitem>
563	<guimenuitem>Mime Types</guimenuitem>
564	</menuchoice>).
565	If a MIME type with the same extension is found and has
566	been connected to a file type, this file type is
567	transferred to the file. This will obviously only work
568	for non-generic file
569	extensions, <emphasis>eg.</emphasis>, .gpr for GenePix
570	raw data files, .cel for Affymetrix CEL files, etc.
571	</para>
572	</answer>
573	</qandaentry>
574	</qandaset>
575
576	</sect1>
577
578	<sect1 id="faqs.data_repositories">
579	<title>Data Deposition to Public Repositories related questions with answers</title>
580	<qandaset defaultlabel='qanda'>
581	<?dbhtml cellspacing="0px" cellpadding="0px" ?>
582	<qandaentry>
583	<question>
584	<para>
585	I am asked by reviewers to deposit my microarray data in a public
586	repository. How can BASE2 help me?
587	</para>
588	</question>
589	<answer>
590	<para>
591	The BASE2 development team are working on a plug-in
592	that produces a Tab2Mage file accepted by ArrayExpress.
593	For the plug-in to work properly, a series of rules need to be
594	followed, please refer to
595	<xref linkend="experiments_analysis.magexport" />
596	for additional information.
597	</para>
598	<para>
599	More information about the Tab2Mage format can be found at
600	<ulink url="http://tab2mage.sourceforge.net"
601	>http://tab2mage.sourceforge.net</ulink>.
602	To send the submission to array express, use the ArrayExpress FTP site
603	at <ulink url="ftp://ftp.ebi.ac.uk pwd">ftp://ftp.ebi.ac.uk pwd</ulink>.
604	Log in with username and password <userinput>aexpress</userinput>.
605	</para>
606	<warning>
607	<para>
608	The current export plug-in does not support Tab2Mage normalised and
609	transformed files, so some additional work might be required to be
610	fully compliant, please refer to Tab2Mage help notes for creating
611	these final gene expression files and update the Tab2Mage files.
612	</para>
613	</warning>
614	</answer>
615	</qandaentry>
616
617	<qandaentry>
618	<question>
619	<para>
620	Repositories want me to be MIAME compliant but how do I know that?
621	</para>
622	</question>
623	<answer>
624	<itemizedlist>
625	<listitem>
626	<para>
627	Make sure to format your annotation types following the rules
628	detailed in <xref linkend="experiments_analysis.magexport" />.
629	</para>
630	</listitem>
631	<listitem>
632	<para>
633	Before exporting, it is probably a good idea to run the
634	<guilabel>Experiment Overview</guilabel>
635	detailed in
636	<xref linkend="experiments_analysis.experiment.overview" />.
637	By selecting stringent criteria from the interface, the tool will
638	detect all missing information that could be requested by
639	repositories.
640	</para>
641	</listitem>
642	<listitem>
643	<para>
644	If the experiment overview does not report any error any more,
645	you can run the Tab2Mage export plug-in suitable for ArrayExpress.
646	</para>
647	</listitem>
648	</itemizedlist>
649	</answer>
650	</qandaentry>
651
652	<qandaentry>
653	<question>
654	<para>
655	I have exported in Tab2Mage file, does it mean I am MIAME compliant?
656	</para>
657	</question>
658	<answer>
659	<para>
660	No, not necessarily! Tab2Mage exporter complies with Tab2Mage
661	specifications so you will be Tab2Mage compliant. However, MIAME
662	compliance depends very much on the kind of annotation you have
663	supplied. Please refer to the previous question for more information
664	about how to check for MIAME compliance in BASE2 using the Experiment
665	overview function.
666	</para>
667	</answer>
668	</qandaentry>
669
670	<qandaentry>
671	<question>
672	<para>
673	I have deleted the data files from BASE2 file systems since I have
674	imported them in tables. So I do not have data files to send to
675	ArrayExpress anymore.
676	</para>
677	</question>
678	<answer>
679	<para>
680	You can export the data from the tables again. Go to the
681	<guilabel>Raw data</guilabel> tab for each of the
682	raw bioassays you need to export. Use the
683	&gbExport; button to export the data. See
684	<xref linkend="import_export_data.export.table_export" />.
685	for more information.
686	</para>
687	</answer>
688	</qandaentry>
689
690	<qandaentry>
691	<question>
692	<para>
693	I have created pooled samples in BASE2. Can I export in Tab2Mage format?
694	</para>
695	</question>
696	<answer>
697	<para>
698	No, sorry, not for the moment. The
699	Tab2Mage exporter does not support pooling events. We are working on
700	adding this features in future version of the plug-in.
701	</para>
702	</answer>
703	</qandaentry>
704	</qandaset>
705	</sect1>
706
707	<sect1 id="faqs.analysis">
708	<title>Analysis related questions with answers</title>
709	<qandaset defaultlabel='qanda'>
710	<?dbhtml cellspacing="0px" cellpadding="0px" ?>
711	<qandaentry>
712	<question>
713	<para>
714	Is it possible to use the formula filter to filter for
715	<constant>null</constant>
716	values (or non-<constant>null</constant> values)?
717	</para>
718	</question>
719	<answer>
720	<para>
721	It is possible to trick the system to filter out <constant>null</constant>
722	values but not non-<constant>null</constant> values. Use an expression like:
723	<userinput>ch(1) == 0 \|\| ch(1) != 0</userinput>. This will match
724	all values, except <constant>null</constant> values.
725	</para>
726	</answer>
727	</qandaentry>
728
729	<qandaentry>
730	<question>
731	<para>
732	OK, I have uploaded 40 CEL files in BASE2 but are there any tool to
733	perform normalisation on Affymetrix raw data?
734	</para>
735	</question>
736	<answer>
737	<para>
738	Yes, there is. BASE2 team has created a plug-in based on
739	<ulink url="http://rmaexpress.bmbolstad.com/">
740	RMAExpress methods from Bolstad and Irizarry</ulink> so you can normalise
741	Affymetrix data sets of reasonable size (not 1000 CEL files at a time
742	though even though this might depend on your set-up...)
743	The plug-in is not included in a standard BASE installation, but
744	can be downloaded from the <ulink url="http://lev.thep.lu.se/trac/baseplugins"
745	>BASE plug-ins web site</ulink>.
746	</para>
747	</answer>
748	</qandaentry>
749	</qandaset>
750	</sect1>
751
752	</chapter>
753
754	</part>

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