source: trunk/doc/src/docbook/faq/faqs.xml @ 3487

Last change on this file since 3487 was 3487, checked in by Peter Johansson, 15 years ago

added end-of-line style property and replaced don't and similiar with do not and corresponding expression

File size: 21.6 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>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 cannot 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 do not 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 do not 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 &amp; 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="biomaterials.samples.create" />.
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 do not 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 do not 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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