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

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<part id="faqs">
  <?dbhtml dir="faqs"?>
  <title>FAQs</title>
  <chapter id="faqs.global">
    <title>Frequently Asked Questions</title>
    <para />
    <sect1 id="faqs.global.reporter">
      <title>Reporters related FAQs</title>
      <qandaset defaultlabel='qanda'>
        <qandaentry>
          <question>
            <simpara>
              I can't find my favourite database for annotating Reporters. Can I add
              my database to BASE2 and if so, How should it proceed?
            </simpara>
          </question>
          <answer>
            <simpara>
              Yes, you can add resources to annotate Reporters. You will need to
              upgrade BASE2 and you may have to contact your system administrator for
              doing so.
            </simpara>

            <simpara>
              In order to change, remove or add annotations fields attached to
              Reporters, you will need modify the extended-properties.xml file and run
              a BASE update. Please refer to section
              <xref linkend="installation_upgrade.installation" />
              for information about both processes. Once done with the upgrade, you'll
              have to defined a new reporter import plugin. Instructions can be found
              under
              <xref linkend="plugins" />
            </simpara>
          </answer>
        </qandaentry>

        <qandaentry>
          <question>
            <simpara>
              I have made a mistake while loading my reporters. How can I delete them
              all in one go ?
            </simpara>
          </question>
          <answer>
            <simpara>
              Please contact your system administrator (maybe in the future use the
              reporter import plugin in delete mode)
            </simpara>
            <note>
              <simpara>
                Common problem: from the gui, one can only delete elements displayed
                from one given pages so how does one do in order to delete several
                thousands of reporters spread across several pages ?
              </simpara>
            </note>
          </answer>
        </qandaentry>
      </qandaset>
    </sect1>

    <sect1 id="faqs.global.arraydesign">
      <title>ArrayDesign related FAQs</title>
      <qandaset defaultlabel='qanda'>
        <qandaentry>
          <question>
            <para>
              I have 20 Affymetrix ArrayDesigns to create from CDF files, is there a
              way to speed-up the creation process ?
            </para>
          </question>
          <answer>
            <para>
              Yes, you can use the Affymetrix CDF ArrayDesign plugin to do so. The
              plugin takes as argument as zipped archive containing CDF or CLF or
              BPMAP files. and then creates all ArrayDesign objects in BASE using the
              CDF files basename as Object Name.
              <note>
                <para>
                  The plugin should be used by Power User or Administrators only.
                </para>
              </note>
            </para>
          </answer>
        </qandaentry>

        <qandaentry>
          <question>
            <para>What about gal files, is there something similar?</para>
          </question>
          <answer>
            <para>
              No, not quite yet as things are a bit more complicated. People are
              working on a plugin for help data entry.
            </para>
          </answer>
        </qandaentry>

        <qandaentry>
          <question>
            <para>
              So What it the best way to create an ArrayDesign in BASE2 when starting
              from a gal file ?
            </para>
          </question>
          <answer>
            <para>
              Ok, this is a bit more work that with Affymetrix but here is the
              procedure to remember:
            </para>
            <para>
              A gal file tells where
              <guilabel>Reporters</guilabel>
              have been spotted on a Array. So a gal file can be used to do 2 things
            </para>
            <orderedlist>
              <listitem>
                <para>
                  -Define the features of an Array Design for a non-Affy platform
                  using a
                  <guilabel>Reporter Map importer plugin</guilabel>
                  .
                </para>
                <para>
                  To do so, after having created an New Array Design, go to the
                  Array Design Item view by clicking on the name of the newly
                  created Array Design
                </para>
                <para>
                  Click on the
                  &gbImport;
                  in the button. If you don't see it, it means that you have not
                  enough priviledges (contact the administrator)
                </para>
                <para>
                  This starts a plugin whose setting should be 'Reporter map
                  importer' and ' the file format should be 'gal file' (note this
                  has to been defined, if not present, please create the proper
                  reporter map plugin configuration.
                </para>
                <para>
                  Now, select File and fill in necessary information from the
                  wizard and run the plugin.
                </para>
                <para>
                  Once done (and if everything went fine), you can see from the
                  Array Design list view that on the Array Design list view page,
                  the
                  <guilabel>Has features</guilabel>
                  entry has been modified and is set to 'Yes (n)' where n
                  indicates the number of spots (features) for this array
                </para>
                <note>
                  <para>
                    Features can also be loaded from a Genepix gpr file
                    according to a very similar procedure but you will have to
                    create a specific reporter map importer plugin configuration
                    for such file before being able to proceed
                  </para>
                </note>
              </listitem>
              <listitem>
                <para>
                  -Define the
                  <guilabel>Reporters</guilabel>
                  present on this Array Design using
                  <guilabel>Reporter importer plugin</guilabel>
                  .
                </para>
                <para>
                  To do so, Go to View, Reporters, click on
                  &gbImport;
                  . This starts a
                  <guilabel>Reporter Importer Plugin</guilabel>
                </para>
                <para>
                  More information about importing Reporters can be found in
                  <xref linkend="reporters" />
                </para>
              </listitem>
            </orderedlist>
          </answer>
        </qandaentry>

        <qandaentry>
          <question>
            <para>
              I am confused. What is the difference between
              <guilabel>Reporter map importer</guilabel>
              ,
              <guilabel>Print map importer</guilabel>
              ' and
              <guilabel>Reporter importer</guilabel>
              ?
            </para>
          </question>
          <answer>
            <para>
              Simple, A Reporter map importer plugin is used toload the Features
              associated to an ArrayDesign. It allows you to understand where a
              Reporter has been spotted on a microarray glass slide
            </para>

            <para>
              A Reporter importer plugin should be used to load Reporter information
              into BASE2
            </para>
            <para>
              A Print Map importer plugin allows to understand which PCR plates where
              used and from which plate a Reporter came from. 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.
              http://www.flychip.org.uk/protocols/robotic_spotting/fileformats.php 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>
          </answer>
        </qandaentry>
      </qandaset>
    </sect1>

    <sect1 id="faqs.global.biomaterial">
      <title>Biomaterial,Protocol, Hardware, Software related FAQS</title>
      <qandaset defaultlabel='qanda'>
        <note>
          <para>
            Note for BASE developers: BioSource pages implement a generic template that
            seems to indicate that Protocols and inherited annotations can be associated
            to BioSource Element. This should be modified. see distinction between
            primary and inherited annotations, and the protocol parameter tag from the
            annotation tab interface.
          </para>
        </note>

        <note>
          <para>It is not possible to sort of the field from the Item view.</para>
        </note>
        <qandaentry>
          <question>
            <para>
              I have just created a new Item (A Sample in my case) but I can not see
              it. Am I doing something wrong ?
            </para>
          </question>
          <answer>
            <para>
              Try clearing the filter. To do so: use the
              <guilabel>view / presets</guilabel>
              dropdown and select the
              <guilabel>clear filter</guilabel>
              entry. This will remove all characters in the search boxes and all
              preselection of item in the drop down lists. If this does not solve your
              problem, then check if the filter displays the item
              <guilabel>owned by me</guilabel>
              .
            </para>
          </answer>
        </qandaentry>

        <qandaentry>
          <question>
            <para>
              I can only see 3 columns from the Biosource List View but I know I have
              a lot more information. Is there a way I can customize the column
              display?
            </para>
          </question>
          <answer>
            <para>
              Yes, you can display many more columns. To do so, do the following:
            </para>
            <para>
              Click on the
              <guibutton>Column</guibutton>
              in the button bar. This will display a window allowing you to select
              which fields to display and in which order. For more information about
              this feature, please refer to the following section of the help note:
              <xref linkend="webclient.figures.configure_columns" />
              Note that in BASE2, The same mechanism applies to all items.
            </para>
          </answer>
        </qandaentry>

        <qandaentry>
          <question>
            <para>
              Is it possible to sort the values in a column from the Item List View?
            </para>
          </question>
          <answer>
            <para>
              Of course it is. You can even sort on multiple columns. Please refer to
              the help section for more information.
              <xref linkend="webclient.itemlist.filter" />
            </para>
          </answer>
        </qandaentry>

        <qandaentry>
          <question>
            <para>
              Is it possible to sort the Annotation Types from Annotation tab in the
              Biosource Item view
            </para>
          </question>
          <answer>
            <para>No. This is not possible at the moment. The page is static.</para>
          </answer>
        </qandaentry>

        <qandaentry>
          <question>
            <para>
              I have to create pools of samples in my experiment due to scarcity of
              the biological material. Can I represent those pooled samples is BASE2?
            </para>
          </question>
          <answer>
            <para>
              Yes, you can. This is a new features in BASE2 over BASE1. BASE2
              graphical user interface features
              <guibutton>Pool...</guibutton>
              button and Samples can be created from other samples. Please refer to
              the following section of the help note:
              <xref linkend="sample.manage.createsample.pool" />
              Note that in BASE2, Pooling events can be represented for Samples,
              Extracts and Labeled Extracts.
            </para>
          </answer>
        </qandaentry>
        <qandaentry>
          <question>
            <para>
              I would like to add a Software Type in BASE2 but there is no button for
              doing so. Is it possible ?
            </para>
          </question>
          <answer>
            <para>
              No, this is not possible. in BASE2, there is only one type of software
              at the moment.
            </para>
          </answer>
        </qandaentry>

        <qandaentry>
          <question>
            <para>
              I need to create a new Hardware type but the
              &gbNew;
              button is grey and does not work. Why?
            </para>
          </question>
          <answer>
            <para>
              Your priviledges are not high enough and you have not been granted
              permission to create Hardware Type. Contact your BASE2 administrator for
              reviewing your priviledges.
            </para>
            <para>To check your current priviledges, do the following</para>
            <para>
              Go to
              <menuchoice>
                <guimenu>Administrate</guimenu>
                <guimenuitem>User</guimenuitem>
              </menuchoice>
              use the search box under
              <guilabel>name</guilabel>
              or
              <guilabel>login</guilabel>
              or
              <guilabel>email</guilabel>
              with relevant information to get to your login details.
            </para>
            <para>In the roles, columns, click on the hyperlinked value.</para>
            <para>
              For more information about permissions, please refer to the dedicated
              help page
              <xref linkend="user_administration" />
            </para>
          </answer>
        </qandaentry>
        <qandaentry>
          <question>
            <para>
              I have created an Annotation Type 'Temperature' and shared it to
              everyone but when I want to use it for annotating a Sample, I can not
              find it ! How is that ?
            </para>
          </question>
          <answer>
            <para>
              The most likely explanation for this is that this particular Annotation
              Type has been declared as Parameter. This means that it will only be
              displayed in BASE2 when calling a protocols. Conversely, Should you have
              declared an Annotation Type as regular one , it would not be made
              available from the list of Possible Paramaters when declaring a
              Protocol.
            </para>
          </answer>
        </qandaentry>

        <qandaentry>
          <question>
            <para>
              I have created an Annotation Type to annotate my samples, but I still
              need to create another 40. Is there a way to speed up the manual entry ?
            </para>
          </question>
          <answer>
            <para>
              Yes. There is a CV loader plugin meant to just perform this tasks and
              batch load your annotation types. You will have to create a tab
              delimited files following a specified format detailed in help section
              <xref linkend="annotations.manage.batchupload" />
              . Once done, simply import the file using the right plugin.
            </para>
          </answer>
        </qandaentry>

        <qandaentry>
          <question>
            <para>
              When importing my Annotation Types from file, I made a mistake and all
              are declared as parameters. How can I fix this?
            </para>
          </question>
          <answer>
            <para>
              Easy. Just modify your input file changing the parameter to no wherever
              needed and run an import in update mode. This will change the values
              stored in BASE2 to the one you want.
            </para>
          </answer>
        </qandaentry>

        <qandaentry>
          <question>
            <para>
              I have read that I could batch-import an Experiment but I can not see
              the
              &gbImport;
              button from the interface. Why?
            </para>
          </question>
          <answer>
            <para>There are possible 2 explanations:</para>
            <orderedlist>
              <listitem>
                <para>
                  The import plugin is not installed on your BASE system. You
                  therefore need to contact your BASE2 administrator or if you
                  have the proper permissions you will have to install a plugin.
                  More information about the plugin installation can be found in
                  <xref linkend="plugins.installation" />
                </para>
              </listitem>
              <listitem>
                <para>
                  The import plugin is installed but you have no permissions for
                  using it. Contact your system administrator and refer to the
                  dedicated help page
                  <xref linkend="user_administration" />
                </para>
              </listitem>
            </orderedlist>
          </answer>
        </qandaentry>

        <qandaentry>
          <question>
            <para>
              I have carried out an experiment using both Affymetrix and Agilent
              arrays but I can not select more than one raw data type in BASE2. What
              should I do ?
            </para>
          </question>
          <answer>
            <para>
              In this particular case and because you are using 2 different raw data
              file formats, you will have to split your experiment in 2. One
              experiment for those samples processed using Affymetrix platform and
              another one using Agilent platform. You don't necessarily have to
              provide all information about the samples again but simply create new
              raw bioassay data which can be grouped in a new experiment.
            </para>
            <para>
              This is an important issue to bear in mind when creating Experiments in
              BASE2
            </para>
          </answer>
        </qandaentry>
      </qandaset>
    </sect1>

    <sect1 id="faqs.global.datafiles_rawdata">
      <title>Data Files and Raw Data related FAQs</title>
      <qandaset defaultlabel='qanda'>
        <qandaentry>
          <question>
            <para>What are the file formats supported by BASE2 ?</para>
          </question>
          <answer>
            <para>
              Please, refer to sections
              <xref linkend="experiments_analysis.rawdatatypes" />
              and
              <xref linkend="appendix.rawdatatypes" />
              for the full list of supported file formats
            </para>
          </answer>
        </qandaentry>

        <qandaentry>
          <question>
            <para>
              It seems that BASE2 does not support the datafiles generated by my brand
              new scanner. Is it possible to add it to BASE2 ?
            </para>
          </question>
          <answer>
            <para>
              Yes it is possible to extend BASE2 so that it can support your system.
            </para>
            <para>
              You will need first to define a new raw data type for BASE2 by modifying
              the raw-datatypes.xml configuration file.
            </para>
            <para>
              Then, you will have to perform an upgrade of the system. See section
              <xref linkend="installation_upgrade" />
            </para>
            <para>
              Finally, you will have to configure a raw data import plugin in order to
              be able to create rawbioassays, refer to sections
              <xref linkend="plugins.configuration" />
              and
              <xref linkend="experiments_analysis" />
              for further information.
            </para>
          </answer>
        </qandaentry>

        <qandaentry>
          <question>
            <para>
              I have created a raw bioassay which is not Affy but the system does not
              allow me to upload a datafile whereas it is possible to do so if I
              declared my rawbioassay of type Affy. Why?
            </para>
          </question>
          <answer>
            <para>
              This is normal. BASE2 deals with Affymetrix datafiles differently. BASE2
              stores native Affymetrix file and does not load the value in tables as
              it does for other platforms.
            </para>
            <para>
              For non-affymetrix rawbioassay, you will have to import the raw data
              files and to do this you will need 3 things:
            </para>
            <orderedlist>
              <listitem>
                <para>
                  - have imported reporters attached to the array design, please
                  refer to the relevant help section here
                  <xref linkend="reporters" />
                  and
                  <xref linkend="array_lims" />
                </para>
              </listitem>
              <listitem>
                <para>
                  - to make sure that your BASE2 instance is configured to support
                  the file format. please refer to BASE2 configuration help page
                </para>
              </listitem>
              <listitem>
                <para>
                  - need a rawdata import plugin properly configured, refer to
                  section for more
                  <xref linkend="plugins.configuration" />
                  <note>
                    <para>
                      Note also that it is possible to import plugin
                      configuration as xml file. Please check the BASE2 page
                      maintaining a
                      <ulink
                        url="http://base.thep.lu.se/chrome/site/doc/admin/plugin_configuration/coreplugins.html">
                        list of plugin configurations
                      </ulink>
                    </para>
                  </note>
                </para>
              </listitem>
            </orderedlist>
          </answer>
        </qandaentry>

        <qandaentry>
          <question>
            <para>
              I have created a raw bioassay using Affymetrix CEL file but the
              interface says 'no spot'. I have really loaded the file ! Why ?
            </para>
          </question>
          <answer>
            <para>
              Again, this is because of the specific treatement of Affymetrix files
              compared to other platforms. Please refer to FAQ 3 and help page
              <xref linkend="experiments_analysis.rawbioassay.rawdata" />
            </para>
          </answer>
        </qandaentry>

        <qandaentry>
          <question>
            <para>Are Affymetrix CTT and CAB files supported by BASE2 ?</para>
          </question>
          <answer>
            <para>
              There is no support for ddt or cab. Currently only cdf and cel files are
              supported by the Affymetrix plug-ins. Annotation files (.csv) are used
              for uploading probeset (reporter in BASE language) information. The
              issue of supporting ddt and cab files is an import and a plug-in issue.
              There are two ways to solve this: i) Write code that treats the file in
              a proper way and submit the solution to the developer team (preferred
              route ;-) ). ii) Submit a ticket through
              <ulink url="http://base.thep.lu.se">http://base.thep.lu.se</ulink>
              explaining what you'd like to see wrt to ddt and cabs. Note, to include
              ddt and cab support to BASE, the file formats must be open, that is we
              must be able to read them without proprietary non-distributable code.
            </para>
          </answer>
        </qandaentry>

        <qandaentry>
          <question>
            <para>Are Illumina datafiles supported by BASE2 ?</para>
          </question>
          <answer>
            <para>
              Yes, thanks to BASE2 user communities, you can find the following
              information
            </para>
            <para>
              Illumina conversion.txt (1.8 kB) - an R script to convert a multi-array
              Illumina .csv output file into multiple single-array files.
            </para>
            <para>
              raw-data-types.xml (92.0 kB) - Raw data types files edited by Jeremy
              Davis-Turak (UCLA Department of Neurology) to include Illumina arrays
            </para>
            <para>
              extended-properties.xml (5.2 kB) - Extended properties file edited by
              Jeremy Davis-Turak (UCLA Department of Neurology) to include reporter
              columns used by Illumina
            </para>
            <para>
              see
              <ulink url="http://base.thep.lu.se/ticket/486">ticket 486</ulink>
              for more information and download the files
            </para>
          </answer>
        </qandaentry>

        <qandaentry>
          <question>
            <para>
              What About Agilent Files, the interface says they are not supported ?
            </para>
          </question>
          <answer>
            <para>
              Yes, thanks to BASE2 user communities, you can find the following
              information
            </para>
          </answer>
        </qandaentry>

        <qandaentry>
          <question>
            <para>
              What About Agilent Files, the interface says they are not supported ?
            </para>
          </question>
          <answer>
            <para>
              Yes, thanks to BASE2 user communities, you can find the following
              information
            </para>
          </answer>
        </qandaentry>
      </qandaset>
    </sect1>

    <sect1 id="faqs.global.data_repositories">
      <title>Data Deposition to Public Repositories related FAQs</title>
      <qandaset defaultlabel='qanda'>
        <qandaentry>
          <question>
            <para>
              I am asked by reviewers to deposit my microarray data in a public
              repository. How can BASE2 help me ?
            </para>
          </question>
          <answer>
            <para>
              BASE2 has an export plugin which produces a tab2mage file accepted by
              ArrayExpress.
            </para>
            <para>
              However, for the plugin to work properly, a series of rules need to be
              followed, please refer to section
              <xref linkend="annotations" />
              for additionnal information.
            </para>
            <para>
              Once tab2mage file successfully exported, you will have to create an
              archive containing all raw datafiles related to the experiment you want
              to sent to ArrayExpress, with tab2mage file. More information about
              tab2mage format can be found
              <ulink url="tab2mage.sourceforge.net">here</ulink>
            </para>
            <para>
              to send the submission to array express, use the following details:
              <ulink url="ftp.ebi.ac.uk pwd">ArrayExpress FTP site</ulink>
              , using login and password 'aexpress'.
            </para>
            <warning>
              <para>
                The current export plugin does not support tab2mage normalized and
                transformed files, so some additional work might be required to be
                fully complient, please refer to tab2mage helpnotes for creating
                these final gene expression files and update the tab2mage files
              </para>
            </warning>
          </answer>
        </qandaentry>

        <qandaentry>
          <question>
            <para>
              Repositories want me to be MIAME compliant but How do i know that ?
            </para>
          </question>
          <answer>
            <para>
              BASE2 can help you in many ways to achieve MIAME compliance and
              therefore facilitate your submissions
            </para>
            <para>
              First, make sure to format your Annotation Types following the rules
              detailed in
              <xref linkend="annotations.bestpractices" />
            </para>
            <para>
              Then, before exporting, it is probably a good idee to run the
              <guilabel>Experiment Overview</guilabel>
              detailed in
              <xref linkend="experiments_analysis.experiment.overview" />
              . By selecting stringent criteria from the interface, the tool will
              detect all missing information that could be requested by Repositories
            </para>
            <para>
              Finally, if the Experiment Overview does not report any error any more,
              you can run the tab2mage export plugin suitable for ArrayExpress at EBI
            </para>
          </answer>
        </qandaentry>

        <qandaentry>
          <question>
            <para>
              I have exported in Tab2mage file, does it mean I am MIAME compliant ?
            </para>
          </question>
          <answer>
            <para>
              NO, not necessarily! Tab2mage exporter complies with Tab2mage
              specifications so you will be Tab2mage compliant. 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.
            </para>
          </answer>
        </qandaentry>

        <qandaentry>
          <question>
            <para>
              I have deleted the datafiles from BASE2 file systems since I have
              imported them in tables. So I don't have datafiles to send to
              ArrayExpress anymore.
            </para>
          </question>
          <answer>
            <para>
              This is not a good news. In the absence of a data exporter, it is
              advised to keep the native datafiles generated by scanners on the file
              system and to name RawBioassays with the datafile names associated with
              it. This ensures an easy tab2mage export.
            </para>
          </answer>
        </qandaentry>

        <qandaentry>
          <question>
            <para>
              I have created pooled samples in BASE2. Can I export in tab2mage format
              ?
            </para>
          </question>
          <answer>
            <para>
              No, sorry, not for the moment. In its current implementation, BASE2
              tab2mage exporter does not support Pooling events. We are working on
              adding this features in future version of the plugin. So watch the BASE2
              plugin space for upgrades.
            </para>
          </answer>
        </qandaentry>
      </qandaset>
    </sect1>

    <sect1 id="faqs.global.analysis">
      <title>Analysis related FAQs</title>
      <qandaset defaultlabel='qanda'>
        <qandaentry>
          <question>
            <para>
              Is it possible to use the FormulaFilter to filter for null fields (or
              non null fields)?
            </para>
          </question>
          <answer>
            <para></para>
          </answer>
        </qandaentry>

        <qandaentry>
          <question>
            <para>
              OK, I have uploaded 40 CEL files in BASE2 but are there any tool to
              perform normalization on Affymetrix raw data ?
            </para>
          </question>
          <answer>
            <para>
              Yes, there is. BASE2 team has created a plugin based on
              <ulink url="http://rmaexpress.bmbolstad.com/">here</ulink>
              RMAExpress methods from Bolstad and Irizarry so you can normalize
              Affymetrix datasets of reasonable size (not 1000 CEL files at a time
              though even though this might depend on your set-up...)
            </para>
            <para>
              Additionnally, thanks to BASE2 web services, you can access BASE2
              remotely from R environment running on more powerfull machine for
              example. This can give you more flexibility for performing normalization
              on large Affymetrix data sets.
            </para>
            <note>
              <para>
                The web service currently only works for Affymetrix raw bioassays
              </para>
            </note>
          </answer>
        </qandaentry>
      </qandaset>
    </sect1>
  </chapter>
</part>