source: trunk/doc/src/docbook/userdoc/faqs.xml @ 3373

Last change on this file since 3373 was 3373, checked in by Martin Svensson, 16 years ago

Correct some small compiling errors

File size: 32.9 KB
1<?xml version="1.0" encoding="UTF-8"?>
3    "-//Dawid Weiss//DTD DocBook V3.1-Based Extension for XML and graphics inclusion//EN"
4    "../../../../lib/docbook/preprocess/dweiss-docbook-extensions.dtd">
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6        $Id: faqs.xml 3246 2007-04-16 14:12:23Z martin $
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29<chapter id="faqs">
30    <?dbhtml dir="faqs"?>
31    <title>FAQs</title>
32    <sect1 id="">
33        <title>Frequently Asked Questions</title>
34        <para/>
37        <sect2 id="">
38            <title>Reporters related FAQs</title>
39            <itemizedlist>
41                <listitem>
43                    <para> Q: I can't find my favourite database for annotating Reporters. Can I add my database to
44                        BASE2 and if so, How should it proceed? </para>
45                    <para> A: Yes, you can add resources to annotate Reporters. You will need to
46                        upgrade BASE2 and you may have to contact your system administrator for
47                        doing so. </para>
48                    <para>In order to change, remove or add annotations fields attached to
49                        Reporters, you will need modify the extended-properties.xml file and run a
50                        BASE update. Please refer to section <xref
51                            linkend="installation_upgrade.installation"/> for information about both
52                        processes. Once done with the upgrade, you'll have to defined a new reporter
53                        import plugin. Instructions can be found under <xref linkend="plugins"/>
54                    </para>
56                </listitem>
58                <listitem>
59                    <para> Q: I have made a mistake while loading my reporters. How can I delete
60                        them all in one go ? </para>
61                    <para> A: Please contact your system administrator (maybe in the future use the
62                        reporter import plugin in delete mode) </para>
63                    <note>
64                        <para> Common problem: from the gui, one can only delete elements displayed
65                            from one given pages so how does one do in order to delete several
66                            thousands of reporters spread across several pages ? </para>
67                    </note>
69                </listitem>
71            </itemizedlist>
72        </sect2>
75        <sect2 id="">
76            <title>ArrayDesign related FAQs</title>
77            <itemizedlist>
78                <listitem>
79                    <para> Q: I have 20 Affymetrix ArrayDesigns to create from CDF files, is there a
80                        way to speed-up the creation process ?</para>
81                    <para> A: Yes, you can use the Affymetrix CDF ArrayDesign plugin to do so. The
82                        plugin takes as argument as zipped archive containing CDF or CLF or BPMAP
83                        files. and then creates all ArrayDesign objects in BASE using the CDF files
84                        basename as Object Name. <note>
85                            <para> The plugin should be used by Power User or Administrators only.
86                            </para>
87                        </note>
88                    </para>
89                </listitem>
91                <listitem>
92                    <para> Q: What about gal files, is there something similar?</para>
93                    <para> A: No, not quite yet as things are a bit more complicated. People are
94                        working on a plugin for help data entry. </para>
95                </listitem>
97                <listitem>
98                    <para> Q: So What it the best way to create an ArrayDesign in BASE2 when
99                        starting from a gal file ?</para>
100                    <para> A: Ok, this is a bit more work that with Affymetrix but here is the
101                        procedure to remember: </para>
102                    <para>A gal file tells where <guilabel>Reporters</guilabel> have been spotted on
103                        a Array. So a gal file can be used to do 2 things</para>
104                    <orderedlist>
105                        <listitem>
106                            <para>-Define the features of an Array Design for a non-Affy
107                                platform using a <guilabel>Reporter Map importer plugin</guilabel>.</para>
108                            <para>To do so, after having created an New Array Design, go to the
109                                Array Design Item view by clicking on the name of the newly created
110                                Array Design</para>
111                            <para>Click on the <guibutton>Import</guibutton> in the button. If you
112                                don't see it, it means that you have not enough priviledges (contact
113                                the administrator)</para>
114                            <para>This starts a plugin whose setting should be 'Reporter map
115                                importer' and ' the file format should be 'gal file' (note this has
116                                to been defined, if not present, please create the proper reporter
117                                map plugin configuration. </para>
118                            <para>Now, select File and fill in necessary information from the wizard
119                                and run the plugin.</para>
120                            <para>Once done (and if everything went fine), you can see from the
121                                Array Design list view that on the Array Design list view page, the
122                                <guilabel>Has features</guilabel> entry has been modified and is
123                                set to 'Yes (n)' where n indicates the number of spots (features)
124                                for this array</para>
125                            <note>
126                                <para>Features can also be loaded from a Genepix gpr file according
127                                    to a very similar procedure but you will have to create a
128                                    specific reporter map importer plugin configuration for such
129                                    file before being able to proceed</para>
130                            </note>
131                        </listitem>
132                        <listitem>
133                            <para>-Define the <guilabel>Reporters</guilabel> present on this Array
134                                Design using <guilabel>Reporter importer plugin</guilabel>. </para>
135                            <para>To do so, Go to View, Reporters, click on
136                                <guibutton>Import</guibutton>. This starts a <guilabel>Reporter
137                                    Importer Plugin</guilabel></para>
138                            <para>More information about importing Reporters can be found in <xref
139                                linkend="reporters"/>
140                            </para>
141                        </listitem>
142                    </orderedlist>
143                </listitem>
145                <listitem>
146                    <para> Q: I am confused. What is the difference between <guilabel>Reporter map importer</guilabel>, <guilabel>Print map importer</guilabel>' and
147                        <guilabel>Reporter importer</guilabel>?</para>
148                    <para> A: Simple, A Reporter map importer plugin is used toload the Features associated to an ArrayDesign.
149                        It allows you to understand where a Reporter has been spotted on a microarray glass slide </para>
151                    <para>A Reporter importer plugin should be used to load Reporter information into BASE2 </para>
152                    <para>A Print Map importer plugin allows to understand which PCR plates where used and from which plate a Reporter came from.
153                    The print map importer supports two formats: Biorobotics TAM format and Molecularware MWBR format. Theese are mapping files that connects plates with features and contains more or less only a bunch of coordinates.
154                        has a good description of both file formats.  So if you are only using commercial platforms or if you don't use plates in the array lims, you have no need for the print map importer.</para>
155                </listitem>
157            </itemizedlist>
158        </sect2>
163        <sect2 id="">
164            <title>Biomaterial,Protocol, Hardware, Software related FAQS</title>
165            <note>
166                <para> Note for BASE developers: BioSource pages implement a generic template that
167                    seems to indicate that Protocols and inherited annotations can be associated to
168                    BioSource Element. This should be modified. see distinction between primary and
169                    inherited annotations, and the protocol parameter tag from the annotation tab
170                    interface. </para>
171            </note>
173            <note>
174                <para> It is not possible to sort of the field from the Item view. </para>
175            </note>
177            <itemizedlist>
179                <listitem>
180                    <para> Q: I have just created a new Item (A Sample in my case) but I can not see
181                        it. Am I doing something wrong ? </para>
182                    <para> A: Try clearing the filter. To do so: use the <guilabel>view /
183                        presets</guilabel> dropdown and select the <guilabel>clear filter</guilabel>
184                        entry. This will remove all characters in the search boxes and all
185                        preselection of item in the drop down lists. If this does not solve your
186                        problem, then check if the filter displays the item <guilabel>owned by
187                        me</guilabel>. </para>
188                </listitem>
190                <listitem>
191                    <para> Q: I can only see 3 columns from the Biosource List View but I know I
192                        have a lot more information. Is there a way I can customize the column display? </para>
193                    <para> A: Yes, you can display many more columns. To do so, do the following:</para>
194                    <para>Click on the <guibutton>Column</guibutton> in the button bar. This will
195                        display a window allowing you to select which fields to display and in
196                        which order. For more information about this feature, please refer to the following section of the help note:
197                            <xref linkend="webclient.figures.configure_columns"/> Note that in
198                        BASE2, The same mechanism applies to all items. </para>
199                </listitem>
201                <listitem>
202                    <para> Q: Is it possible to sort the values in a column from the Item List
203                        View? </para>
204                    <para> A: Of course it is. You can even sort on multiple columns. Please refer to the
205                        help section for more information. <xref linkend="webclient.itemlist.filter"
206                        />
207                    </para>
208                </listitem>
210                <listitem>
211                    <para> Q: Is it possible to sort the Annotation Types from Annotation tab in the
212                        Biosource Item view </para>
213                    <para> A: No. This is not possible at the moment. The page is static. </para>
214                </listitem>
216                <listitem>
217                    <para> Q: I have to create pools of samples in my experiment due to scarcity of the biological material. Can I represent those pooled samples is
218                        BASE2? </para>
219                    <para> A: Yes, you can. This is a new features in BASE2 over BASE1. BASE2
220                        graphical user interface features <guibutton>Pool...</guibutton> button and
221                        Samples can be created from other samples. Please refer to the following
222                        section of the help note: <xref linkend="sample.manage.createsample.pool"/>
223                        Note that in BASE2, Pooling events can be represented for Samples, Extracts
224                        and Labeled Extracts. </para>
225                </listitem>
227                <listitem>
228                    <para> Q: I would like to add a Software Type in BASE2 but there is no button
229                        for doing so. Is it possible ? </para>
230                    <para> A: No, this is not possible. in BASE2, there is only one type of software at the moment.
231                    </para>
232                </listitem>
234                <listitem>
235                    <para> Q: I need to create a new Hardware type but the
236                        <guibutton>New...</guibutton>button is grey and does not work. Why? </para>
238                    <para>A: Your priviledges are not high enough and you have not been granted
239                        permission to create Hardware Type. Contact your BASE2 administrator for
240                        reviewing your priviledges.</para>
241                    <para>To check your current priviledges, do the following</para>
242                    <para> Go to <menuchoice>
243                            <guimenu>Administrate</guimenu>
244                            <guimenuitem>User</guimenuitem>
245                        </menuchoice> use the search box under <guilabel>name</guilabel> or
246                            <guilabel>login</guilabel> or <guilabel>email</guilabel> with relevant
247                        information to get to your login details.</para>
248                    <para> In the roles, columns, click on the hyperlinked value.</para>
249                    <para> For more information about permissions, please refer to the dedicated
250                        help page<xref linkend="user_administration"/>
251                    </para>
252                </listitem>
255                <listitem>
256                    <para> Q: I have created an Annotation Type 'Temperature' and shared it to
257                        everyone but when I want to use it for annotating a Sample, I can not find
258                        it ! How is that ? </para>
259                    <para> A: The most likely explanation for this is that this particular
260                        Annotation Type has been declared as Parameter. This means that it will only
261                        be displayed in BASE2 when calling a protocols. Conversely, Should you have
262                        declared an Annotation Type as regular one , it would not be made available
263                        from the list of Possible Paramaters when declaring a Protocol. </para>
264                </listitem>
266                <listitem>
267                    <para> Q: I have created an Annotation Type to annotate my samples, but I still
268                        need to create another 40. Is there a way to speed up the manual entry ? </para>
269                    <para> A: Yes. There is a CV loader plugin meant to just perform this tasks and
270                        batch load your annotation types. You will have to create a tab delimited
271                        files following a specified format detailed in help section <xref
272                            linkend="annotations.manage.batchupload"/>. Once done, simply import the
273                        file using the right plugin. </para>
274                </listitem>
276                <listitem>
277                    <para> Q: When importing my Annotation Types from file, I made a mistake and all
278                        are declared as parameters. How can I fix this? </para>
279                    <para> A: Easy. Just modify your input file changing the parameter to no
280                        wherever needed and run an import in update mode. This will change the
281                        values stored in BASE2 to the one you want. </para>
282                </listitem>
284                <listitem>
285                    <para>Q: I have read that I could batch-import an Experiment but I can not see
286                        the <guibutton>import</guibutton> button from the interface. Why?</para>
288                    <para>A: There are possible 2 explanations:</para>
289                    <orderedlist>
290                        <listitem>
291                            <para>The import plugin is not installed on your BASE system. You
292                                therefore need to contact your BASE2 administrator or if you have
293                                the proper permissions you will have to install a plugin. More
294                                information about the plugin installation can be found in <xref
295                                    linkend="plugins.installation"/>
296                            </para>
297                        </listitem>
298                        <listitem>
299                            <para>The import plugin is installed but you have no permissions for
300                                using it. Contact your system administrator and refer to the
301                                dedicated help page <xref linkend="user_administration"/>
302                            </para>
303                        </listitem>
304                    </orderedlist>
305                </listitem>
307                <listitem>
308                    <para> Q: I have carried out an experiment using both Affymetrix and Agilent
309                        arrays but I can not select more than one raw data type in BASE2. What
310                        should I do ? </para>
311                    <para> A: In this particular case and because you are using 2 different raw data
312                        file formats, you will have to split your experiment in 2. One experiment
313                        for those samples processed using Affymetrix platform and another one using
314                        Agilent platform. You don't necessarily have to provide all information
315                        about the samples again but simply create new raw bioassay data which can be
316                        grouped in a new experiment. </para>
317                    <para> This is an important issue to bear in mind when creating Experiments in
318                        BASE2</para>
319                </listitem>
321            </itemizedlist>
322        </sect2>
324        <sect2 id="">
325            <title>Data Files and Raw Data related FAQs</title>
326            <orderedlist>
328                <listitem>
329                    <para> Q: What are the file formats supported by BASE2 ? </para>
330                    <para> A: Please, refer to sections <xref
331                        linkend="experiments_analysis.rawdatatypes"/> and <xref
332                            linkend="appendix.rawdatatypes"/>for the full list of
333                        supported file formats </para>
334                </listitem>
336                <listitem>
337                    <para> Q: It seems that BASE2 does not support the datafiles generated by my
338                        brand new scanner. Is it possible to add it to BASE2 ? </para>
339                    <para> A: Yes it is possible to extend BASE2 so that it can support your system.</para>
340                    <para>You will need first to define a new raw data type for BASE2 by modifying
341                        the raw-datatypes.xml configuration file. </para>
342                    <para>Then, you will have to perform an upgrade of the system. See section <xref
343                            linkend="installation_upgrade"/></para>
344                    <para>Finally, you will have to configure a raw data import plugin in order to
345                        be able to create rawbioassays, refer to sections <xref
346                            linkend="plugins.configuration"/> and <xref
347                            linkend="experiments_analysis"/> for further information. </para>
348                </listitem>
350                <listitem>
351                    <para> Q: I have created a raw bioassay which is not Affy but the system does
352                        not allow me to upload a datafile whereas it is possible to do so if I
353                        declared my rawbioassay of type Affy. Why? </para>
354                    <para>A: This is normal. BASE2 deals with Affymetrix datafiles differently.
355                        BASE2 stores native Affymetrix file and does not load the value in tables as
356                        it does for other platforms.</para>
357                    <para> For non-affymetrix rawbioassay, you will have to import the raw data
358                        files and to do this you will need 3 things:</para>
359                    <orderedlist>
360                        <listitem>
361                            <para> - have imported reporters attached to the array design, please
362                                refer to the relevant help section here <xref linkend="reporters"/>
363                                and <xref linkend="array_lims"/>
364                            </para>
365                        </listitem>
366                        <listitem>
367                            <para> - to make sure that your BASE2 instance is configured to support
368                                the file format. please refer to BASE2 configuration help page
369                            </para>
370                        </listitem>
371                        <listitem>
372                            <para> - need a rawdata import plugin properly configured, refer to
373                                section for more <xref linkend="plugins.configuration"/>
374                                <note>
375                                    <para>Note also that it is possible to import plugin
376                                        configuration as xml file. Please check the BASE2 page
377                                        maintaining a <ulink
378                                            url=""
379                                            >list of plugin configurations</ulink>
380                                    </para>
381                                </note>
382                            </para>
383                        </listitem>
384                    </orderedlist>
385                </listitem>
386                <listitem>
387                    <para> Q: I have created a raw bioassay using Affymetrix CEL file but the
388                        interface says 'no spot'. I have really loaded the file ! Why ? </para>
389                    <para> A: Again, this is because of the specific treatement of Affymetrix files
390                        compared to other platforms. Please refer to FAQ 3 and help page <xref
391                            linkend="experiments_analysis.rawbioassay.rawdata"/>
392                    </para>
393                </listitem>
395                <listitem>
396                    <para> Q: Are Affymetrix CTT and CAB files supported by BASE2 ? </para>
397                    <para> A: There is no support for ddt or cab. Currently only cdf and cel files
398                        are supported by the Affymetrix plug-ins. Annotation files (.csv) are used
399                        for uploading probeset (reporter in BASE language) information. The issue of
400                        supporting ddt and cab files is an import and a plug-in issue. There are two
401                        ways to solve this: i) Write code that treats the file in a proper way and
402                        submit the solution to the developer team (preferred route ;-) ). ii) Submit
403                        a ticket through <ulink url=""
404                        ></ulink> explaining what you'd like to see wrt to ddt
405                        and cabs. Note, to include ddt and cab support to BASE, the file formats
406                        must be open, that is we must be able to read them without proprietary
407                        non-distributable code. </para>
408                </listitem>
411                <listitem>
412                    <para> Q: Are Illumina datafiles supported by BASE2 ? </para>
413                    <para> A: Yes, thanks to BASE2 user communities, you can find the following
414                        information </para>
415                    <para> Illumina conversion.txt (1.8 kB) - an R script to convert a multi-array
416                        Illumina .csv output file into multiple single-array files.</para>
417                    <para> raw-data-types.xml (92.0 kB) - Raw data types files edited by Jeremy
418                        Davis-Turak (UCLA Department of Neurology) to include Illumina arrays</para>
419                    <para>extended-properties.xml (5.2 kB) - Extended properties file edited by
420                        Jeremy Davis-Turak (UCLA Department of Neurology) to include reporter
421                        columns used by Illumina</para>
422                    <para>see <ulink url="">ticket 486</ulink> for
423                        more information and download the files</para>
424                </listitem>
426                <listitem>
427                    <para> Q: What About Agilent Files, the interface says they are not supported ? </para>
428                    <para> A: Yes, thanks to BASE2 user communities, you can find the following
429                        information </para>
430                </listitem>
433                <listitem>
434                    <para> Q: What About Agilent Files, the interface says they are not supported ? </para>
435                    <para> A: Yes, thanks to BASE2 user communities, you can find the following
436                        information </para>
437                </listitem>
439            </orderedlist>
440        </sect2>
442        <sect2 id="">
443            <title>Data Deposition to Public Repositories related FAQs</title>
445            <itemizedlist>
446                <listitem>
447                    <para> Q: I am asked by reviewers to deposit my microarray data in a public
448                        repository. How can BASE2 help me ? </para>
449                    <para> A: BASE2 has an export plugin which produces a tab2mage file accepted by
450                        ArrayExpress. </para>
451                    <para> However, for the plugin to work properly, a series of rules need to be
452                        followed, please refer to section <xref linkend="annotations"/> for
453                        additionnal information. </para>
454                    <para> Once tab2mage file successfully exported, you will have to create an
455                        archive containing all raw datafiles related to the experiment you want to
456                        sent to ArrayExpress, with tab2mage file. More information about tab2mage
457                        format can be found <ulink url="">here</ulink></para>
458                    <para> to send the submission to array express, use the following details:
459                            <ulink url=" pwd">ArrayExpress FTP site</ulink>, using
460                        login and password 'aexpress'. </para>
461                    <warning>
462                        <para> The current export plugin does not support tab2mage normalized and
463                            transformed files, so some additional work might be required to be fully
464                            complient, please refer to tab2mage helpnotes for creating these final
465                            gene expression files and update the tab2mage files </para>
466                    </warning>
468                </listitem>
470                <listitem>
471                    <para>Q: Repositories want me to be MIAME compliant but How do i know that ?</para>
472                    <para>A: BASE2 can help you in many ways to achieve MIAME compliance and
473                        therefore facilitate your submissions</para>
474                    <para>First, make sure to format your Annotation Types following the rules
475                        detailed in <xref linkend="annotations.bestpractices"/></para>
476                    <para>Then, before exporting, it is probably a good idee to run the
477                            <guilabel>Experiment Overview</guilabel> detailed in <xref
478                            linkend="experiments_analysis.experiment.overview"/>. By selecting
479                        stringent criteria from the interface, the tool will detect all missing
480                        information that could be requested by Repositories</para>
481                    <para>Finally, if the Experiment Overview does not report any error any more,
482                        you can run the tab2mage export plugin suitable for ArrayExpress at
483                    EBI</para>
484                </listitem>
486                <listitem>
487                    <para>
488                        Q: I have exported in Tab2mage file, does it mean I am MIAME compliant ?
489                    </para>
490                    <para>
491                        A: NO, not necessarily! Tab2mage exporter complies with Tab2mage specifications so you will be Tab2mage compliant.
492                        However, MIAME compliance depends very much on the kind of annotation you have supplied. Please refer to the previous question for more information about how to check for MIAME compliance in BASE2 using the Experiment overview function.
493                    </para>
494                </listitem>
498                <listitem>
499                    <para> Q: I have deleted the datafiles from BASE2 file systems since I have
500                        imported them in tables. So I don't have datafiles to send to ArrayExpress
501                        anymore. </para>
502                    <para> A: This is not a good news. In the absence of a data exporter, it is
503                        advised to keep the native datafiles generated by scanners on the file
504                        system and to name RawBioassays with the datafile names associated with it.
505                        This ensures an easy tab2mage export. </para>
506                </listitem>
508                <listitem>
509                    <para> Q: I have created pooled samples in BASE2. Can I export in tab2mage
510                        format ? </para>
511                    <para> A: No, sorry, not for the moment. In its current implementation, BASE2
512                        tab2mage exporter does not support Pooling events. We are working on adding
513                        this features in future version of the plugin. So watch the BASE2 plugin
514                        space for upgrades. </para>
515                </listitem>
517            </itemizedlist>
518        </sect2>
522        <sect2 id="">
523            <title>Analysis related FAQs</title>
524            <itemizedlist>
526                <listitem>
527                    <para> Q:Is it possible to use the FormulaFilter to filter for null fields (or
528                        non null fields)? </para>
529                    <para> A: </para>
530                </listitem>
532                <listitem>
533                    <para> Q:OK, I have uploaded 40 CEL files in BASE2 but are there any tool to
534                        perform normalization on Affymetrix raw data ? </para>
535                    <para> A: Yes, there is. BASE2 team has created a plugin based on
536                        <ulink url="">here</ulink>
537                                              RMAExpress methods
538                        from Bolstad and Irizarry so you can normalize Affymetrix datasets of reasonable
539                        size (not 1000 CEL files at a time though even though this might depend on your set-up...) </para>
540                    <para>Additionnally, thanks to BASE2 web services, you can access BASE2 remotely
541                        from R environment running on more powerfull machine for example. This can
542                        give you more flexibility for performing normalization on large Affymetrix
543                        data sets. </para>
544                    <note>
545                        <para>The web service currently only works for Affymetrix raw bioassays
546                        </para>
547                    </note>
548                </listitem>
550            </itemizedlist>
551        </sect2>
553    </sect1>
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