source: trunk/doc/src/docbook/faq/faqs.xml @ 3394

Last change on this file since 3394 was 3394, checked in by Martin Svensson, 15 years ago

Replaced the most common guibutton:s with entities

File size: 29.2 KB
Line 
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>FAQs</title>
32  <chapter id="faqs.global">
33    <title>Frequently Asked Questions</title>
34    <para />
35    <sect1 id="faqs.global.reporter">
36      <title>Reporters related FAQs</title>
37      <qandaset defaultlabel='qanda'>
38        <qandaentry>
39          <question>
40            <simpara>
41              I can't find my favourite database for annotating Reporters. Can I add
42              my database to BASE2 and if so, How should it proceed?
43            </simpara>
44          </question>
45          <answer>
46            <simpara>
47              Yes, you can add resources to annotate Reporters. You will need to
48              upgrade BASE2 and you may have to contact your system administrator for
49              doing so.
50            </simpara>
51
52            <simpara>
53              In order to change, remove or add annotations fields attached to
54              Reporters, you will need modify the extended-properties.xml file and run
55              a BASE update. Please refer to section
56              <xref linkend="installation_upgrade.installation" />
57              for information about both processes. Once done with the upgrade, you'll
58              have to defined a new reporter import plugin. Instructions can be found
59              under
60              <xref linkend="plugins" />
61            </simpara>
62          </answer>
63        </qandaentry>
64
65        <qandaentry>
66          <question>
67            <simpara>
68              I have made a mistake while loading my reporters. How can I delete them
69              all in one go ?
70            </simpara>
71          </question>
72          <answer>
73            <simpara>
74              Please contact your system administrator (maybe in the future use the
75              reporter import plugin in delete mode)
76            </simpara>
77            <note>
78              <simpara>
79                Common problem: from the gui, one can only delete elements displayed
80                from one given pages so how does one do in order to delete several
81                thousands of reporters spread across several pages ?
82              </simpara>
83            </note>
84          </answer>
85        </qandaentry>
86      </qandaset>
87    </sect1>
88
89    <sect1 id="faqs.global.arraydesign">
90      <title>ArrayDesign related FAQs</title>
91      <qandaset defaultlabel='qanda'>
92        <qandaentry>
93          <question>
94            <para>
95              I have 20 Affymetrix ArrayDesigns to create from CDF files, is there a
96              way to speed-up the creation process ?
97            </para>
98          </question>
99          <answer>
100            <para>
101              Yes, you can use the Affymetrix CDF ArrayDesign plugin to do so. The
102              plugin takes as argument as zipped archive containing CDF or CLF or
103              BPMAP files. and then creates all ArrayDesign objects in BASE using the
104              CDF files basename as Object Name.
105              <note>
106                <para>
107                  The plugin should be used by Power User or Administrators only.
108                </para>
109              </note>
110            </para>
111          </answer>
112        </qandaentry>
113
114        <qandaentry>
115          <question>
116            <para>What about gal files, is there something similar?</para>
117          </question>
118          <answer>
119            <para>
120              No, not quite yet as things are a bit more complicated. People are
121              working on a plugin for help data entry.
122            </para>
123          </answer>
124        </qandaentry>
125
126        <qandaentry>
127          <question>
128            <para>
129              So What it the best way to create an ArrayDesign in BASE2 when starting
130              from a gal file ?
131            </para>
132          </question>
133          <answer>
134            <para>
135              Ok, this is a bit more work that with Affymetrix but here is the
136              procedure to remember:
137            </para>
138            <para>
139              A gal file tells where
140              <guilabel>Reporters</guilabel>
141              have been spotted on a Array. So a gal file can be used to do 2 things
142            </para>
143            <orderedlist>
144              <listitem>
145                <para>
146                  -Define the features of an Array Design for a non-Affy platform
147                  using a
148                  <guilabel>Reporter Map importer plugin</guilabel>
149                  .
150                </para>
151                <para>
152                  To do so, after having created an New Array Design, go to the
153                  Array Design Item view by clicking on the name of the newly
154                  created Array Design
155                </para>
156                <para>
157                  Click on the
158                  &gbImport;
159                  in the button. If you don't see it, it means that you have not
160                  enough priviledges (contact the administrator)
161                </para>
162                <para>
163                  This starts a plugin whose setting should be 'Reporter map
164                  importer' and ' the file format should be 'gal file' (note this
165                  has to been defined, if not present, please create the proper
166                  reporter map plugin configuration.
167                </para>
168                <para>
169                  Now, select File and fill in necessary information from the
170                  wizard and run the plugin.
171                </para>
172                <para>
173                  Once done (and if everything went fine), you can see from the
174                  Array Design list view that on the Array Design list view page,
175                  the
176                  <guilabel>Has features</guilabel>
177                  entry has been modified and is set to 'Yes (n)' where n
178                  indicates the number of spots (features) for this array
179                </para>
180                <note>
181                  <para>
182                    Features can also be loaded from a Genepix gpr file
183                    according to a very similar procedure but you will have to
184                    create a specific reporter map importer plugin configuration
185                    for such file before being able to proceed
186                  </para>
187                </note>
188              </listitem>
189              <listitem>
190                <para>
191                  -Define the
192                  <guilabel>Reporters</guilabel>
193                  present on this Array Design using
194                  <guilabel>Reporter importer plugin</guilabel>
195                  .
196                </para>
197                <para>
198                  To do so, Go to View, Reporters, click on
199                  &gbImport;
200                  . This starts a
201                  <guilabel>Reporter Importer Plugin</guilabel>
202                </para>
203                <para>
204                  More information about importing Reporters can be found in
205                  <xref linkend="reporters" />
206                </para>
207              </listitem>
208            </orderedlist>
209          </answer>
210        </qandaentry>
211
212        <qandaentry>
213          <question>
214            <para>
215              I am confused. What is the difference between
216              <guilabel>Reporter map importer</guilabel>
217              ,
218              <guilabel>Print map importer</guilabel>
219              ' and
220              <guilabel>Reporter importer</guilabel>
221              ?
222            </para>
223          </question>
224          <answer>
225            <para>
226              Simple, A Reporter map importer plugin is used toload the Features
227              associated to an ArrayDesign. It allows you to understand where a
228              Reporter has been spotted on a microarray glass slide
229            </para>
230
231            <para>
232              A Reporter importer plugin should be used to load Reporter information
233              into BASE2
234            </para>
235            <para>
236              A Print Map importer plugin allows to understand which PCR plates where
237              used and from which plate a Reporter came from. The print map importer
238              supports two formats: Biorobotics TAM format and Molecularware MWBR
239              format. Theese are mapping files that connects plates with features and
240              contains more or less only a bunch of coordinates.
241              http://www.flychip.org.uk/protocols/robotic_spotting/fileformats.php has
242              a good description of both file formats. So if you are only using
243              commercial platforms or if you don't use plates in the array lims, you
244              have no need for the print map importer.
245            </para>
246          </answer>
247        </qandaentry>
248      </qandaset>
249    </sect1>
250
251    <sect1 id="faqs.global.biomaterial">
252      <title>Biomaterial,Protocol, Hardware, Software related FAQS</title>
253      <qandaset defaultlabel='qanda'>
254        <note>
255          <para>
256            Note for BASE developers: BioSource pages implement a generic template that
257            seems to indicate that Protocols and inherited annotations can be associated
258            to BioSource Element. This should be modified. see distinction between
259            primary and inherited annotations, and the protocol parameter tag from the
260            annotation tab interface.
261          </para>
262        </note>
263
264        <note>
265          <para>It is not possible to sort of the field from the Item view.</para>
266        </note>
267        <qandaentry>
268          <question>
269            <para>
270              I have just created a new Item (A Sample in my case) but I can not see
271              it. Am I doing something wrong ?
272            </para>
273          </question>
274          <answer>
275            <para>
276              Try clearing the filter. To do so: use the
277              <guilabel>view / presets</guilabel>
278              dropdown and select the
279              <guilabel>clear filter</guilabel>
280              entry. This will remove all characters in the search boxes and all
281              preselection of item in the drop down lists. If this does not solve your
282              problem, then check if the filter displays the item
283              <guilabel>owned by me</guilabel>
284              .
285            </para>
286          </answer>
287        </qandaentry>
288
289        <qandaentry>
290          <question>
291            <para>
292              I can only see 3 columns from the Biosource List View but I know I have
293              a lot more information. Is there a way I can customize the column
294              display?
295            </para>
296          </question>
297          <answer>
298            <para>
299              Yes, you can display many more columns. To do so, do the following:
300            </para>
301            <para>
302              Click on the
303              <guibutton>Column</guibutton>
304              in the button bar. This will display a window allowing you to select
305              which fields to display and in which order. For more information about
306              this feature, please refer to the following section of the help note:
307              <xref linkend="webclient.figures.configure_columns" />
308              Note that in BASE2, The same mechanism applies to all items.
309            </para>
310          </answer>
311        </qandaentry>
312
313        <qandaentry>
314          <question>
315            <para>
316              Is it possible to sort the values in a column from the Item List View?
317            </para>
318          </question>
319          <answer>
320            <para>
321              Of course it is. You can even sort on multiple columns. Please refer to
322              the help section for more information.
323              <xref linkend="webclient.itemlist.filter" />
324            </para>
325          </answer>
326        </qandaentry>
327
328        <qandaentry>
329          <question>
330            <para>
331              Is it possible to sort the Annotation Types from Annotation tab in the
332              Biosource Item view
333            </para>
334          </question>
335          <answer>
336            <para>No. This is not possible at the moment. The page is static.</para>
337          </answer>
338        </qandaentry>
339
340        <qandaentry>
341          <question>
342            <para>
343              I have to create pools of samples in my experiment due to scarcity of
344              the biological material. Can I represent those pooled samples is BASE2?
345            </para>
346          </question>
347          <answer>
348            <para>
349              Yes, you can. This is a new features in BASE2 over BASE1. BASE2
350              graphical user interface features
351              <guibutton>Pool...</guibutton>
352              button and Samples can be created from other samples. Please refer to
353              the following section of the help note:
354              <xref linkend="sample.manage.createsample.pool" />
355              Note that in BASE2, Pooling events can be represented for Samples,
356              Extracts and Labeled Extracts.
357            </para>
358          </answer>
359        </qandaentry>
360        <qandaentry>
361          <question>
362            <para>
363              I would like to add a Software Type in BASE2 but there is no button for
364              doing so. Is it possible ?
365            </para>
366          </question>
367          <answer>
368            <para>
369              No, this is not possible. in BASE2, there is only one type of software
370              at the moment.
371            </para>
372          </answer>
373        </qandaentry>
374
375        <qandaentry>
376          <question>
377            <para>
378              I need to create a new Hardware type but the
379              &gbNew;
380              button is grey and does not work. Why?
381            </para>
382          </question>
383          <answer>
384            <para>
385              Your priviledges are not high enough and you have not been granted
386              permission to create Hardware Type. Contact your BASE2 administrator for
387              reviewing your priviledges.
388            </para>
389            <para>To check your current priviledges, do the following</para>
390            <para>
391              Go to
392              <menuchoice>
393                <guimenu>Administrate</guimenu>
394                <guimenuitem>User</guimenuitem>
395              </menuchoice>
396              use the search box under
397              <guilabel>name</guilabel>
398              or
399              <guilabel>login</guilabel>
400              or
401              <guilabel>email</guilabel>
402              with relevant information to get to your login details.
403            </para>
404            <para>In the roles, columns, click on the hyperlinked value.</para>
405            <para>
406              For more information about permissions, please refer to the dedicated
407              help page
408              <xref linkend="user_administration" />
409            </para>
410          </answer>
411        </qandaentry>
412        <qandaentry>
413          <question>
414            <para>
415              I have created an Annotation Type 'Temperature' and shared it to
416              everyone but when I want to use it for annotating a Sample, I can not
417              find it ! How is that ?
418            </para>
419          </question>
420          <answer>
421            <para>
422              The most likely explanation for this is that this particular Annotation
423              Type has been declared as Parameter. This means that it will only be
424              displayed in BASE2 when calling a protocols. Conversely, Should you have
425              declared an Annotation Type as regular one , it would not be made
426              available from the list of Possible Paramaters when declaring a
427              Protocol.
428            </para>
429          </answer>
430        </qandaentry>
431
432        <qandaentry>
433          <question>
434            <para>
435              I have created an Annotation Type to annotate my samples, but I still
436              need to create another 40. Is there a way to speed up the manual entry ?
437            </para>
438          </question>
439          <answer>
440            <para>
441              Yes. There is a CV loader plugin meant to just perform this tasks and
442              batch load your annotation types. You will have to create a tab
443              delimited files following a specified format detailed in help section
444              <xref linkend="annotations.manage.batchupload" />
445              . Once done, simply import the file using the right plugin.
446            </para>
447          </answer>
448        </qandaentry>
449
450        <qandaentry>
451          <question>
452            <para>
453              When importing my Annotation Types from file, I made a mistake and all
454              are declared as parameters. How can I fix this?
455            </para>
456          </question>
457          <answer>
458            <para>
459              Easy. Just modify your input file changing the parameter to no wherever
460              needed and run an import in update mode. This will change the values
461              stored in BASE2 to the one you want.
462            </para>
463          </answer>
464        </qandaentry>
465
466        <qandaentry>
467          <question>
468            <para>
469              I have read that I could batch-import an Experiment but I can not see
470              the
471              &gbImport;
472              button from the interface. Why?
473            </para>
474          </question>
475          <answer>
476            <para>There are possible 2 explanations:</para>
477            <orderedlist>
478              <listitem>
479                <para>
480                  The import plugin is not installed on your BASE system. You
481                  therefore need to contact your BASE2 administrator or if you
482                  have the proper permissions you will have to install a plugin.
483                  More information about the plugin installation can be found in
484                  <xref linkend="plugins.installation" />
485                </para>
486              </listitem>
487              <listitem>
488                <para>
489                  The import plugin is installed but you have no permissions for
490                  using it. Contact your system administrator and refer to the
491                  dedicated help page
492                  <xref linkend="user_administration" />
493                </para>
494              </listitem>
495            </orderedlist>
496          </answer>
497        </qandaentry>
498
499        <qandaentry>
500          <question>
501            <para>
502              I have carried out an experiment using both Affymetrix and Agilent
503              arrays but I can not select more than one raw data type in BASE2. What
504              should I do ?
505            </para>
506          </question>
507          <answer>
508            <para>
509              In this particular case and because you are using 2 different raw data
510              file formats, you will have to split your experiment in 2. One
511              experiment for those samples processed using Affymetrix platform and
512              another one using Agilent platform. You don't necessarily have to
513              provide all information about the samples again but simply create new
514              raw bioassay data which can be grouped in a new experiment.
515            </para>
516            <para>
517              This is an important issue to bear in mind when creating Experiments in
518              BASE2
519            </para>
520          </answer>
521        </qandaentry>
522      </qandaset>
523    </sect1>
524
525    <sect1 id="faqs.global.datafiles_rawdata">
526      <title>Data Files and Raw Data related FAQs</title>
527      <qandaset defaultlabel='qanda'>
528        <qandaentry>
529          <question>
530            <para>What are the file formats supported by BASE2 ?</para>
531          </question>
532          <answer>
533            <para>
534              Please, refer to sections
535              <xref linkend="experiments_analysis.rawdatatypes" />
536              and
537              <xref linkend="appendix.rawdatatypes" />
538              for the full list of supported file formats
539            </para>
540          </answer>
541        </qandaentry>
542
543        <qandaentry>
544          <question>
545            <para>
546              It seems that BASE2 does not support the datafiles generated by my brand
547              new scanner. Is it possible to add it to BASE2 ?
548            </para>
549          </question>
550          <answer>
551            <para>
552              Yes it is possible to extend BASE2 so that it can support your system.
553            </para>
554            <para>
555              You will need first to define a new raw data type for BASE2 by modifying
556              the raw-datatypes.xml configuration file.
557            </para>
558            <para>
559              Then, you will have to perform an upgrade of the system. See section
560              <xref linkend="installation_upgrade" />
561            </para>
562            <para>
563              Finally, you will have to configure a raw data import plugin in order to
564              be able to create rawbioassays, refer to sections
565              <xref linkend="plugins.configuration" />
566              and
567              <xref linkend="experiments_analysis" />
568              for further information.
569            </para>
570          </answer>
571        </qandaentry>
572
573        <qandaentry>
574          <question>
575            <para>
576              I have created a raw bioassay which is not Affy but the system does not
577              allow me to upload a datafile whereas it is possible to do so if I
578              declared my rawbioassay of type Affy. Why?
579            </para>
580          </question>
581          <answer>
582            <para>
583              This is normal. BASE2 deals with Affymetrix datafiles differently. BASE2
584              stores native Affymetrix file and does not load the value in tables as
585              it does for other platforms.
586            </para>
587            <para>
588              For non-affymetrix rawbioassay, you will have to import the raw data
589              files and to do this you will need 3 things:
590            </para>
591            <orderedlist>
592              <listitem>
593                <para>
594                  - have imported reporters attached to the array design, please
595                  refer to the relevant help section here
596                  <xref linkend="reporters" />
597                  and
598                  <xref linkend="array_lims" />
599                </para>
600              </listitem>
601              <listitem>
602                <para>
603                  - to make sure that your BASE2 instance is configured to support
604                  the file format. please refer to BASE2 configuration help page
605                </para>
606              </listitem>
607              <listitem>
608                <para>
609                  - need a rawdata import plugin properly configured, refer to
610                  section for more
611                  <xref linkend="plugins.configuration" />
612                  <note>
613                    <para>
614                      Note also that it is possible to import plugin
615                      configuration as xml file. Please check the BASE2 page
616                      maintaining a
617                      <ulink
618                        url="http://base.thep.lu.se/chrome/site/doc/admin/plugin_configuration/coreplugins.html">
619                        list of plugin configurations
620                      </ulink>
621                    </para>
622                  </note>
623                </para>
624              </listitem>
625            </orderedlist>
626          </answer>
627        </qandaentry>
628
629        <qandaentry>
630          <question>
631            <para>
632              I have created a raw bioassay using Affymetrix CEL file but the
633              interface says 'no spot'. I have really loaded the file ! Why ?
634            </para>
635          </question>
636          <answer>
637            <para>
638              Again, this is because of the specific treatement of Affymetrix files
639              compared to other platforms. Please refer to FAQ 3 and help page
640              <xref linkend="experiments_analysis.rawbioassay.rawdata" />
641            </para>
642          </answer>
643        </qandaentry>
644
645        <qandaentry>
646          <question>
647            <para>Are Affymetrix CTT and CAB files supported by BASE2 ?</para>
648          </question>
649          <answer>
650            <para>
651              There is no support for ddt or cab. Currently only cdf and cel files are
652              supported by the Affymetrix plug-ins. Annotation files (.csv) are used
653              for uploading probeset (reporter in BASE language) information. The
654              issue of supporting ddt and cab files is an import and a plug-in issue.
655              There are two ways to solve this: i) Write code that treats the file in
656              a proper way and submit the solution to the developer team (preferred
657              route ;-) ). ii) Submit a ticket through
658              <ulink url="http://base.thep.lu.se">http://base.thep.lu.se</ulink>
659              explaining what you'd like to see wrt to ddt and cabs. Note, to include
660              ddt and cab support to BASE, the file formats must be open, that is we
661              must be able to read them without proprietary non-distributable code.
662            </para>
663          </answer>
664        </qandaentry>
665
666        <qandaentry>
667          <question>
668            <para>Are Illumina datafiles supported by BASE2 ?</para>
669          </question>
670          <answer>
671            <para>
672              Yes, thanks to BASE2 user communities, you can find the following
673              information
674            </para>
675            <para>
676              Illumina conversion.txt (1.8 kB) - an R script to convert a multi-array
677              Illumina .csv output file into multiple single-array files.
678            </para>
679            <para>
680              raw-data-types.xml (92.0 kB) - Raw data types files edited by Jeremy
681              Davis-Turak (UCLA Department of Neurology) to include Illumina arrays
682            </para>
683            <para>
684              extended-properties.xml (5.2 kB) - Extended properties file edited by
685              Jeremy Davis-Turak (UCLA Department of Neurology) to include reporter
686              columns used by Illumina
687            </para>
688            <para>
689              see
690              <ulink url="http://base.thep.lu.se/ticket/486">ticket 486</ulink>
691              for more information and download the files
692            </para>
693          </answer>
694        </qandaentry>
695
696        <qandaentry>
697          <question>
698            <para>
699              What About Agilent Files, the interface says they are not supported ?
700            </para>
701          </question>
702          <answer>
703            <para>
704              Yes, thanks to BASE2 user communities, you can find the following
705              information
706            </para>
707          </answer>
708        </qandaentry>
709
710        <qandaentry>
711          <question>
712            <para>
713              What About Agilent Files, the interface says they are not supported ?
714            </para>
715          </question>
716          <answer>
717            <para>
718              Yes, thanks to BASE2 user communities, you can find the following
719              information
720            </para>
721          </answer>
722        </qandaentry>
723      </qandaset>
724    </sect1>
725
726    <sect1 id="faqs.global.data_repositories">
727      <title>Data Deposition to Public Repositories related FAQs</title>
728      <qandaset defaultlabel='qanda'>
729        <qandaentry>
730          <question>
731            <para>
732              I am asked by reviewers to deposit my microarray data in a public
733              repository. How can BASE2 help me ?
734            </para>
735          </question>
736          <answer>
737            <para>
738              BASE2 has an export plugin which produces a tab2mage file accepted by
739              ArrayExpress.
740            </para>
741            <para>
742              However, for the plugin to work properly, a series of rules need to be
743              followed, please refer to section
744              <xref linkend="annotations" />
745              for additionnal information.
746            </para>
747            <para>
748              Once tab2mage file successfully exported, you will have to create an
749              archive containing all raw datafiles related to the experiment you want
750              to sent to ArrayExpress, with tab2mage file. More information about
751              tab2mage format can be found
752              <ulink url="tab2mage.sourceforge.net">here</ulink>
753            </para>
754            <para>
755              to send the submission to array express, use the following details:
756              <ulink url="ftp.ebi.ac.uk pwd">ArrayExpress FTP site</ulink>
757              , using login and password 'aexpress'.
758            </para>
759            <warning>
760              <para>
761                The current export plugin does not support tab2mage normalized and
762                transformed files, so some additional work might be required to be
763                fully complient, please refer to tab2mage helpnotes for creating
764                these final gene expression files and update the tab2mage files
765              </para>
766            </warning>
767          </answer>
768        </qandaentry>
769
770        <qandaentry>
771          <question>
772            <para>
773              Repositories want me to be MIAME compliant but How do i know that ?
774            </para>
775          </question>
776          <answer>
777            <para>
778              BASE2 can help you in many ways to achieve MIAME compliance and
779              therefore facilitate your submissions
780            </para>
781            <para>
782              First, make sure to format your Annotation Types following the rules
783              detailed in
784              <xref linkend="annotations.bestpractices" />
785            </para>
786            <para>
787              Then, before exporting, it is probably a good idee to run the
788              <guilabel>Experiment Overview</guilabel>
789              detailed in
790              <xref linkend="experiments_analysis.experiment.overview" />
791              . By selecting stringent criteria from the interface, the tool will
792              detect all missing information that could be requested by Repositories
793            </para>
794            <para>
795              Finally, if the Experiment Overview does not report any error any more,
796              you can run the tab2mage export plugin suitable for ArrayExpress at EBI
797            </para>
798          </answer>
799        </qandaentry>
800
801        <qandaentry>
802          <question>
803            <para>
804              I have exported in Tab2mage file, does it mean I am MIAME compliant ?
805            </para>
806          </question>
807          <answer>
808            <para>
809              NO, not necessarily! Tab2mage exporter complies with Tab2mage
810              specifications so you will be Tab2mage compliant. However, MIAME
811              compliance depends very much on the kind of annotation you have
812              supplied. Please refer to the previous question for more information
813              about how to check for MIAME compliance in BASE2 using the Experiment
814              overview function.
815            </para>
816          </answer>
817        </qandaentry>
818
819        <qandaentry>
820          <question>
821            <para>
822              I have deleted the datafiles from BASE2 file systems since I have
823              imported them in tables. So I don't have datafiles to send to
824              ArrayExpress anymore.
825            </para>
826          </question>
827          <answer>
828            <para>
829              This is not a good news. In the absence of a data exporter, it is
830              advised to keep the native datafiles generated by scanners on the file
831              system and to name RawBioassays with the datafile names associated with
832              it. This ensures an easy tab2mage export.
833            </para>
834          </answer>
835        </qandaentry>
836
837        <qandaentry>
838          <question>
839            <para>
840              I have created pooled samples in BASE2. Can I export in tab2mage format
841              ?
842            </para>
843          </question>
844          <answer>
845            <para>
846              No, sorry, not for the moment. In its current implementation, BASE2
847              tab2mage exporter does not support Pooling events. We are working on
848              adding this features in future version of the plugin. So watch the BASE2
849              plugin space for upgrades.
850            </para>
851          </answer>
852        </qandaentry>
853      </qandaset>
854    </sect1>
855
856    <sect1 id="faqs.global.analysis">
857      <title>Analysis related FAQs</title>
858      <qandaset defaultlabel='qanda'>
859        <qandaentry>
860          <question>
861            <para>
862              Is it possible to use the FormulaFilter to filter for null fields (or
863              non null fields)?
864            </para>
865          </question>
866          <answer>
867            <para></para>
868          </answer>
869        </qandaentry>
870
871        <qandaentry>
872          <question>
873            <para>
874              OK, I have uploaded 40 CEL files in BASE2 but are there any tool to
875              perform normalization on Affymetrix raw data ?
876            </para>
877          </question>
878          <answer>
879            <para>
880              Yes, there is. BASE2 team has created a plugin based on
881              <ulink url="http://rmaexpress.bmbolstad.com/">here</ulink>
882              RMAExpress methods from Bolstad and Irizarry so you can normalize
883              Affymetrix datasets of reasonable size (not 1000 CEL files at a time
884              though even though this might depend on your set-up...)
885            </para>
886            <para>
887              Additionnally, thanks to BASE2 web services, you can access BASE2
888              remotely from R environment running on more powerfull machine for
889              example. This can give you more flexibility for performing normalization
890              on large Affymetrix data sets.
891            </para>
892            <note>
893              <para>
894                The web service currently only works for Affymetrix raw bioassays
895              </para>
896            </note>
897          </answer>
898        </qandaentry>
899      </qandaset>
900    </sect1>
901  </chapter>
902</part>
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