Ignore:
Timestamp:
May 29, 2007, 11:21:49 AM (16 years ago)
Author:
Nicklas Nordborg
Message:

Fixed FAQ chapters.

File:
1 edited

Legend:

Unmodified
Added
Removed

  • trunk/doc/src/docbook/faq/faqs.xml

    r3394 r3402  
    2929<part id="faqs">
    3030  <?dbhtml dir="faqs"?>
    31   <title>FAQs</title>
    32   <chapter id="faqs.global">
    33     <title>Frequently Asked Questions</title>
    34     <para />
    35     <sect1 id="faqs.global.reporter">
     31  <title>Frequently Asked Questions</title>
     32
     33    <chapter id="faqs.reporter">
    3634      <title>Reporters related FAQs</title>
    3735      <qandaset defaultlabel='qanda'>
     36        <?dbhtml cellspacing="0px" cellpadding="0px" ?>
    3837        <qandaentry>
    3938          <question>
    4039            <simpara>
    41               I can't find my favourite database for annotating Reporters. Can I add
     40              I can't find my favourite database for annotating reporters. Can I add
    4241              my database to BASE2 and if so, How should it proceed?
    4342            </simpara>
    … …  
    4544          <answer>
    4645            <simpara>
    47               Yes, you can add resources to annotate Reporters. You will need to
     46              Yes, you can add resources to annotate reporters. You will need to
    4847              upgrade BASE2 and you may have to contact your system administrator for
    4948              doing so.
    … …  
    5150
    5251            <simpara>
    53               In order to change, remove or add annotations fields attached to
    54               Reporters, you will need modify the extended-properties.xml file and run
    55               a BASE update. Please refer to section
     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
    5655              <xref linkend="installation_upgrade.installation" />
    5756              for information about both processes. Once done with the upgrade, you'll
    58               have to defined a new reporter import plugin. Instructions can be found
    59               under
    60               <xref linkend="plugins" />
     57              have to defined a new reporter import plug-in. Instructions can be found
     58              in <xref linkend="plugins" />.
    6159            </simpara>
    6260          </answer>
    … …  
    7270          <answer>
    7371            <simpara>
    74               Please contact your system administrator (maybe in the future use the
    75               reporter import plugin in delete mode)
     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.
    7675            </simpara>
    77             <note>
    78               <simpara>
    79                 Common problem: from the gui, one can only delete elements displayed
    80                 from one given pages so how does one do in order to delete several
    81                 thousands of reporters spread across several pages ?
    82               </simpara>
    83             </note>
    8476          </answer>
    8577        </qandaentry>
    8678      </qandaset>
    87     </sect1>
    88 
    89     <sect1 id="faqs.global.arraydesign">
    90       <title>ArrayDesign related FAQs</title>
     79    </chapter>
     80
     81    <chapter id="faqs.arraydesign">
     82      <title>Array design related FAQs</title>
    9183      <qandaset defaultlabel='qanda'>
    92         <qandaentry>
    93           <question>
    94             <para>
    95               I have 20 Affymetrix ArrayDesigns to create from CDF files, is there a
    96               way to speed-up the creation process ?
    97             </para>
    98           </question>
    99           <answer>
    100             <para>
    101               Yes, you can use the Affymetrix CDF ArrayDesign plugin to do so. The
    102               plugin takes as argument as zipped archive containing CDF or CLF or
    103               BPMAP files. and then creates all ArrayDesign objects in BASE using the
    104               CDF files basename as Object Name.
    105               <note>
    106                 <para>
    107                   The plugin should be used by Power User or Administrators only.
    108                 </para>
    109               </note>
    110             </para>
    111           </answer>
    112         </qandaentry>
    113 
    114         <qandaentry>
    115           <question>
    116             <para>What about gal files, is there something similar?</para>
    117           </question>
    118           <answer>
    119             <para>
    120               No, not quite yet as things are a bit more complicated. People are
    121               working on a plugin for help data entry.
    122             </para>
    123           </answer>
    124         </qandaentry>
    125 
    126         <qandaentry>
    127           <question>
    128             <para>
    129               So What it the best way to create an ArrayDesign in BASE2 when starting
    130               from a gal file ?
    131             </para>
    132           </question>
    133           <answer>
    134             <para>
    135               Ok, this is a bit more work that with Affymetrix but here is the
     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
    13695              procedure to remember:
    13796            </para>
    13897            <para>
    139               A gal file tells where
    140               <guilabel>Reporters</guilabel>
    141               have been spotted on a Array. So a gal file can be used to do 2 things
     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
    142100            </para>
    143101            <orderedlist>
    144102              <listitem>
    145103                <para>
    146                   -Define the features of an Array Design for a non-Affy platform
    147                   using a
    148                   <guilabel>Reporter Map importer plugin</guilabel>
    149                   .
    150                 </para>
    151                 <para>
    152                   To do so, after having created an New Array Design, go to the
    153                   Array Design Item view by clicking on the name of the newly
    154                   created Array Design
    155                 </para>
    156                 <para>
    157                   Click on the
    158                   &gbImport;
    159                   in the button. If you don't see it, it means that you have not
    160                   enough priviledges (contact the administrator)
    161                 </para>
    162                 <para>
    163                   This starts a plugin whose setting should be 'Reporter map
    164                   importer' and ' the file format should be 'gal file' (note this
    165                   has to been defined, if not present, please create the proper
    166                   reporter map plugin configuration.
    167                 </para>
    168                 <para>
    169                   Now, select File and fill in necessary information from the
    170                   wizard and run the plugin.
     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 don't 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.
    171124                </para>
    172125                <para>
    173126                  Once done (and if everything went fine), you can see from the
    174                   Array Design list view that on the Array Design list view page,
    175                   the
     127                  Array Design list view that the
    176128                  <guilabel>Has features</guilabel>
    177129                  entry has been modified and is set to 'Yes (n)' where n
    178                   indicates the number of spots (features) for this array
     130                  indicates the number of spots (features) for this array.
    179131                </para>
    180132                <note>
    181133                  <para>
    182                     Features can also be loaded from a Genepix gpr file
    183                     according to a very similar procedure but you will have to
    184                     create a specific reporter map importer plugin configuration
    185                     for such file before being able to proceed
     134                    Features can also be loaded from a Genepix GPR file
     135                    with the same procedure.
    186136                  </para>
    187137                </note>
    … …  
    189139              <listitem>
    190140                <para>
    191                   -Define the
     141                  Define the
    192142                  <guilabel>Reporters</guilabel>
    193                   present on this Array Design using
    194                   <guilabel>Reporter importer plugin</guilabel>
    195                   .
    196                 </para>
    197                 <para>
    198                   To do so, Go to View, Reporters, click on
    199                   &gbImport;
    200                   . This starts a
    201                   <guilabel>Reporter Importer Plugin</guilabel>
     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>
    202155                </para>
    203156                <para>
    … …  
    214167            <para>
    215168              I am confused. What is the difference between
    216               <guilabel>Reporter map importer</guilabel>
    217               ,
    218               <guilabel>Print map importer</guilabel>
    219               ' and
    220               <guilabel>Reporter importer</guilabel>
    221               ?
    222             </para>
    223           </question>
    224           <answer>
    225             <para>
    226               Simple, A Reporter map importer plugin is used toload the Features
    227               associated to an ArrayDesign. It allows you to understand where a
    228               Reporter has been spotted on a microarray glass slide
    229             </para>
    230 
    231             <para>
    232               A Reporter importer plugin should be used to load Reporter information
    233               into BASE2
    234             </para>
    235             <para>
    236               A Print Map importer plugin allows to understand which PCR plates where
    237               used and from which plate a Reporter came from. The print map importer
    238               supports two formats: Biorobotics TAM format and Molecularware MWBR
    239               format. Theese are mapping files that connects plates with features and
    240               contains more or less only a bunch of coordinates.
    241               http://www.flychip.org.uk/protocols/robotic_spotting/fileformats.php has
    242               a good description of both file formats. So if you are only using
    243               commercial platforms or if you don't use plates in the array lims, you
    244               have no need for the print map importer.
     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 don't 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.
    245191            </para>
    246192          </answer>
    247193        </qandaentry>
    248194      </qandaset>
    249     </sect1>
    250 
    251     <sect1 id="faqs.global.biomaterial">
    252       <title>Biomaterial,Protocol, Hardware, Software related FAQS</title>
     195    </chapter>
     196
     197    <chapter id="faqs.biomaterial">
     198      <title>Biomaterial, Protocol, Hardware, Software related FAQS</title>
    253199      <qandaset defaultlabel='qanda'>
    254         <note>
    255           <para>
    256             Note for BASE developers: BioSource pages implement a generic template that
    257             seems to indicate that Protocols and inherited annotations can be associated
    258             to BioSource Element. This should be modified. see distinction between
    259             primary and inherited annotations, and the protocol parameter tag from the
    260             annotation tab interface.
    261           </para>
    262         </note>
    263 
    264         <note>
    265           <para>It is not possible to sort of the field from the Item view.</para>
    266         </note>
    267         <qandaentry>
    268           <question>
    269             <para>
    270               I have just created a new Item (A Sample in my case) but I can not see
    271               it. Am I doing something wrong ?
     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?
    272206            </para>
    273207          </question>
    … …  
    280214              entry. This will remove all characters in the search boxes and all
    281215              preselection of item in the drop down lists. If this does not solve your
    282               problem, then check if the filter displays the item
    283               <guilabel>owned by me</guilabel>
    284               .
    285             </para>
    286           </answer>
    287         </qandaentry>
    288 
    289         <qandaentry>
    290           <question>
    291             <para>
    292               I can only see 3 columns from the Biosource List View but I know I have
     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
    293226              a lot more information. Is there a way I can customize the column
    294227              display?
    … …  
    297230          <answer>
    298231            <para>
    299               Yes, you can display many more columns. To do so, do the following:
    300             </para>
    301             <para>
    302               Click on the
    303               <guibutton>Column</guibutton>
    304               in the button bar. This will display a window allowing you to select
    305               which fields to display and in which order. For more information about
    306               this feature, please refer to the following section of the help note:
    307               <xref linkend="webclient.figures.configure_columns" />
    308               Note that in BASE2, The same mechanism applies to all items.
    309             </para>
    310           </answer>
    311         </qandaentry>
    312 
    313         <qandaentry>
    314           <question>
    315             <para>
    316               Is it possible to sort the values in a column from the Item List View?
    317             </para>
    318           </question>
    319           <answer>
    320             <para>
    321               Of course it is. You can even sort on multiple columns. Please refer to
    322               the help section for more information.
    323               <xref linkend="webclient.itemlist.filter" />
    324             </para>
    325           </answer>
    326         </qandaentry>
    327 
    328         <qandaentry>
    329           <question>
    330             <para>
    331               Is it possible to sort the Annotation Types from Annotation tab in the
    332               Biosource Item view
    333             </para>
    334           </question>
    335           <answer>
    336             <para>No. This is not possible at the moment. The page is static.</para>
     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>
    337264          </answer>
    338265        </qandaentry>
    … …  
    347274          <answer>
    348275            <para>
    349               Yes, you can. This is a new features in BASE2 over BASE1. BASE2
    350               graphical user interface features
    351               <guibutton>Pool...</guibutton>
    352               button and Samples can be created from other samples. Please refer to
    353               the following section of the help note:
    354               <xref linkend="sample.manage.createsample.pool" />
    355               Note that in BASE2, Pooling events can be represented for Samples,
    356               Extracts and Labeled Extracts.
    357             </para>
    358           </answer>
    359         </qandaentry>
    360         <qandaentry>
    361           <question>
    362             <para>
    363               I would like to add a Software Type in BASE2 but there is no button for
    364               doing so. Is it possible ?
    365             </para>
    366           </question>
    367           <answer>
    368             <para>
    369               No, this is not possible. in BASE2, there is only one type of software
    370               at the moment.
    371             </para>
    372           </answer>
    373         </qandaentry>
    374 
    375         <qandaentry>
    376           <question>
    377             <para>
    378               I need to create a new Hardware type but the
     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="sample.manage.createsample.pool" />.
     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
    379304              &gbNew;
    380305              button is grey and does not work. Why?
    … …  
    383308          <answer>
    384309            <para>
    385               Your priviledges are not high enough and you have not been granted
    386               permission to create Hardware Type. Contact your BASE2 administrator for
    387               reviewing your priviledges.
    388             </para>
    389             <para>To check your current priviledges, do the following</para>
    390             <para>
    391               Go to
    392               <menuchoice>
    393                 <guimenu>Administrate</guimenu>
    394                 <guimenuitem>User</guimenuitem>
    395               </menuchoice>
    396               use the search box under
    397               <guilabel>name</guilabel>
    398               or
    399               <guilabel>login</guilabel>
    400               or
    401               <guilabel>email</guilabel>
    402               with relevant information to get to your login details.
    403             </para>
    404             <para>In the roles, columns, click on the hyperlinked value.</para>
    405             <para>
    406               For more information about permissions, please refer to the dedicated
    407               help page
    408               <xref linkend="user_administration" />
    409             </para>
    410           </answer>
    411         </qandaentry>
    412         <qandaentry>
    413           <question>
    414             <para>
    415               I have created an Annotation Type 'Temperature' and shared it to
    416               everyone but when I want to use it for annotating a Sample, I can not
    417               find it ! How is that ?
    418             </para>
    419           </question>
    420           <answer>
    421             <para>
    422               The most likely explanation for this is that this particular Annotation
    423               Type has been declared as Parameter. This means that it will only be
    424               displayed in BASE2 when calling a protocols. Conversely, Should you have
    425               declared an Annotation Type as regular one , it would not be made
    426               available from the list of Possible Paramaters when declaring a
    427               Protocol.
    428             </para>
    429           </answer>
    430         </qandaentry>
    431 
    432         <qandaentry>
    433           <question>
    434             <para>
    435               I have created an Annotation Type to annotate my samples, but I still
    436               need to create another 40. Is there a way to speed up the manual entry ?
    437             </para>
    438           </question>
    439           <answer>
    440             <para>
    441               Yes. There is a CV loader plugin meant to just perform this tasks and
    442               batch load your annotation types. You will have to create a tab
    443               delimited files following a specified format detailed in help section
    444               <xref linkend="annotations.manage.batchupload" />
    445               . Once done, simply import the file using the right plugin.
    446             </para>
    447           </answer>
    448         </qandaentry>
    449 
    450         <qandaentry>
    451           <question>
    452             <para>
    453               When importing my Annotation Types from file, I made a mistake and all
    454               are declared as parameters. How can I fix this?
    455             </para>
    456           </question>
    457           <answer>
    458             <para>
    459               Easy. Just modify your input file changing the parameter to no wherever
    460               needed and run an import in update mode. This will change the values
    461               stored in BASE2 to the one you want.
    462             </para>
    463           </answer>
    464         </qandaentry>
    465 
    466         <qandaentry>
    467           <question>
    468             <para>
    469               I have read that I could batch-import an Experiment but I can not see
    470               the
    471               &gbImport;
    472               button from the interface. Why?
    473             </para>
    474           </question>
    475           <answer>
    476             <para>There are possible 2 explanations:</para>
    477             <orderedlist>
    478               <listitem>
    479                 <para>
    480                   The import plugin is not installed on your BASE system. You
    481                   therefore need to contact your BASE2 administrator or if you
    482                   have the proper permissions you will have to install a plugin.
    483                   More information about the plugin installation can be found in
    484                   <xref linkend="plugins.installation" />
    485                 </para>
    486               </listitem>
    487               <listitem>
    488                 <para>
    489                   The import plugin is installed but you have no permissions for
    490                   using it. Contact your system administrator and refer to the
    491                   dedicated help page
    492                   <xref linkend="user_administration" />
    493                 </para>
    494               </listitem>
    495             </orderedlist>
     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>
    496332          </answer>
    497333        </qandaentry>
    … …  
    502338              I have carried out an experiment using both Affymetrix and Agilent
    503339              arrays but I can not select more than one raw data type in BASE2. What
    504               should I do ?
     340              should I do?
    505341            </para>
    506342          </question>
    … …  
    514350              raw bioassay data which can be grouped in a new experiment.
    515351            </para>
    516             <para>
    517               This is an important issue to bear in mind when creating Experiments in
    518               BASE2
    519             </para>
    520352          </answer>
    521353        </qandaentry>
    522354      </qandaset>
    523     </sect1>
    524 
    525     <sect1 id="faqs.global.datafiles_rawdata">
     355    </chapter>
     356
     357    <chapter id="faqs.datafiles_rawdata">
    526358      <title>Data Files and Raw Data related FAQs</title>
    527359      <qandaset defaultlabel='qanda'>
    528         <qandaentry>
    529           <question>
    530             <para>What are the file formats supported by BASE2 ?</para>
    531           </question>
    532           <answer>
    533             <para>
    534               Please, refer to sections
    535               <xref linkend="experiments_analysis.rawdatatypes" />
    536               and
    537               <xref linkend="appendix.rawdatatypes" />
    538               for the full list of supported file formats
    539             </para>
    540           </answer>
    541         </qandaentry>
    542 
     360        <?dbhtml cellspacing="0px" cellpadding="0px" ?>
    543361        <qandaentry>
    544362          <question>
    545363            <para>
    546364              It seems that BASE2 does not support the datafiles generated by my brand
    547               new scanner. Is it possible to add it to BASE2 ?
     365              new scanner. Is it possible to add it to BASE2?
    548366            </para>
    549367          </question>
    … …  
    551369            <para>
    552370              Yes it is possible to extend BASE2 so that it can support your system.
    553             </para>
    554             <para>
    555               You will need first to define a new raw data type for BASE2 by modifying
    556               the raw-datatypes.xml configuration file.
    557             </para>
    558             <para>
    559               Then, you will have to perform an upgrade of the system. See section
    560               <xref linkend="installation_upgrade" />
    561             </para>
    562             <para>
    563               Finally, you will have to configure a raw data import plugin in order to
    564               be able to create rawbioassays, refer to sections
     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
    565382              <xref linkend="plugins.configuration" />
    566383              and
    567               <xref linkend="experiments_analysis" />
     384              <xref linkend="experiments_analysis.rawbioassay.rawdata" />
    568385              for further information.
    569386            </para>
    … …  
    583400              This is normal. BASE2 deals with Affymetrix datafiles differently. BASE2
    584401              stores native Affymetrix file and does not load the value in tables as
    585               it does for other platforms.
    586             </para>
    587             <para>
    588               For non-affymetrix rawbioassay, you will have to import the raw data
    589               files and to do this you will need 3 things:
    590             </para>
    591             <orderedlist>
     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>
    592438              <listitem>
    593439                <para>
    594                   - have imported reporters attached to the array design, please
    595                   refer to the relevant help section here
    596                   <xref linkend="reporters" />
    597                   and
    598                   <xref linkend="array_lims" />
     440                Write code that treats the files in a proper way and submit
     441                the solution to the developer team (preferred route).
    599442                </para>
    600443              </listitem>
    601444              <listitem>
    602445                <para>
    603                   - to make sure that your BASE2 instance is configured to support
    604                   the file format. please refer to BASE2 configuration help page
     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.
    605449                </para>
    606450              </listitem>
    607               <listitem>
    608                 <para>
    609                   - need a rawdata import plugin properly configured, refer to
    610                   section for more
    611                   <xref linkend="plugins.configuration" />
    612                   <note>
    613                     <para>
    614                       Note also that it is possible to import plugin
    615                       configuration as xml file. Please check the BASE2 page
    616                       maintaining a
    617                       <ulink
    618                         url="http://base.thep.lu.se/chrome/site/doc/admin/plugin_configuration/coreplugins.html">
    619                         list of plugin configurations
    620                       </ulink>
    621                     </para>
    622                   </note>
    623                 </para>
    624               </listitem>
    625             </orderedlist>
    626           </answer>
    627         </qandaentry>
    628 
    629         <qandaentry>
    630           <question>
    631             <para>
    632               I have created a raw bioassay using Affymetrix CEL file but the
    633               interface says 'no spot'. I have really loaded the file ! Why ?
    634             </para>
    635           </question>
    636           <answer>
    637             <para>
    638               Again, this is because of the specific treatement of Affymetrix files
    639               compared to other platforms. Please refer to FAQ 3 and help page
    640               <xref linkend="experiments_analysis.rawbioassay.rawdata" />
    641             </para>
    642           </answer>
    643         </qandaentry>
    644 
    645         <qandaentry>
    646           <question>
    647             <para>Are Affymetrix CTT and CAB files supported by BASE2 ?</para>
    648           </question>
    649           <answer>
    650             <para>
    651               There is no support for ddt or cab. Currently only cdf and cel files are
    652               supported by the Affymetrix plug-ins. Annotation files (.csv) are used
    653               for uploading probeset (reporter in BASE language) information. The
    654               issue of supporting ddt and cab files is an import and a plug-in issue.
    655               There are two ways to solve this: i) Write code that treats the file in
    656               a proper way and submit the solution to the developer team (preferred
    657               route ;-) ). ii) Submit a ticket through
    658               <ulink url="http://base.thep.lu.se">http://base.thep.lu.se</ulink>
    659               explaining what you'd like to see wrt to ddt and cabs. Note, to include
    660               ddt and cab support to BASE, the file formats must be open, that is we
    661               must be able to read them without proprietary non-distributable code.
     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>
    662460            </para>
    663461          </answer>
    … …  
    670468          <answer>
    671469            <para>
    672               Yes, thanks to BASE2 user communities, you can find the following
    673               information
    674             </para>
    675             <para>
    676               Illumina conversion.txt (1.8 kB) - an R script to convert a multi-array
    677               Illumina .csv output file into multiple single-array files.
    678             </para>
    679             <para>
    680               raw-data-types.xml (92.0 kB) - Raw data types files edited by Jeremy
    681               Davis-Turak (UCLA Department of Neurology) to include Illumina arrays
    682             </para>
    683             <para>
    684               extended-properties.xml (5.2 kB) - Extended properties file edited by
    685               Jeremy Davis-Turak (UCLA Department of Neurology) to include reporter
    686               columns used by Illumina
    687             </para>
    688             <para>
    689               see
     470              Not by default, but the BASE user community has provided
     471              a workaround to make it possible.
     472              See
    690473              <ulink url="http://base.thep.lu.se/ticket/486">ticket 486</ulink>
    691               for more information and download the files
    692             </para>
    693           </answer>
    694         </qandaentry>
    695 
    696         <qandaentry>
    697           <question>
    698             <para>
    699               What About Agilent Files, the interface says they are not supported ?
    700             </para>
    701           </question>
    702           <answer>
    703             <para>
    704               Yes, thanks to BASE2 user communities, you can find the following
    705               information
    706             </para>
    707           </answer>
    708         </qandaentry>
    709 
    710         <qandaentry>
    711           <question>
    712             <para>
    713               What About Agilent Files, the interface says they are not supported ?
    714             </para>
    715           </question>
    716           <answer>
    717             <para>
    718               Yes, thanks to BASE2 user communities, you can find the following
    719               information
     474              on the BASE website for more information.
    720475            </para>
    721476          </answer>
    722477        </qandaentry>
    723478      </qandaset>
    724     </sect1>
    725 
    726     <sect1 id="faqs.global.data_repositories">
     479    </chapter>
     480
     481    <chapter id="faqs.data_repositories">
    727482      <title>Data Deposition to Public Repositories related FAQs</title>
    728483      <qandaset defaultlabel='qanda'>
     484        <?dbhtml cellspacing="0px" cellpadding="0px" ?>
    729485        <qandaentry>
    730486          <question>
    731487            <para>
    732488              I am asked by reviewers to deposit my microarray data in a public
    733               repository. How can BASE2 help me ?
    734             </para>
    735           </question>
    736           <answer>
    737             <para>
    738               BASE2 has an export plugin which produces a tab2mage file accepted by
    739               ArrayExpress.
    740             </para>
    741             <para>
    742               However, for the plugin to work properly, a series of rules need to be
    743               followed, please refer to section
    744               <xref linkend="annotations" />
    745               for additionnal information.
    746             </para>
    747             <para>
    748               Once tab2mage file successfully exported, you will have to create an
    749               archive containing all raw datafiles related to the experiment you want
    750               to sent to ArrayExpress, with tab2mage file. More information about
    751               tab2mage format can be found
    752               <ulink url="tab2mage.sourceforge.net">here</ulink>
    753             </para>
    754             <para>
    755               to send the submission to array express, use the following details:
    756               <ulink url="ftp.ebi.ac.uk pwd">ArrayExpress FTP site</ulink>
    757               , using login and password 'aexpress'.
     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>.
    758508            </para>
    759509            <warning>
    760510              <para>
    761                 The current export plugin does not support tab2mage normalized and
     511                The current export plug-in does not support Tab2Mage normalized and
    762512                transformed files, so some additional work might be required to be
    763                 fully complient, please refer to tab2mage helpnotes for creating
    764                 these final gene expression files and update the tab2mage files
     513                fully complient, please refer to Tab2Mage helpnotes for creating
     514                these final gene expression files and update the Tab2Mage files.
    765515              </para>
    766516            </warning>
    … …  
    771521          <question>
    772522            <para>
    773               Repositories want me to be MIAME compliant but How do i know that ?
    774             </para>
    775           </question>
    776           <answer>
    777             <para>
    778               BASE2 can help you in many ways to achieve MIAME compliance and
    779               therefore facilitate your submissions
    780             </para>
    781             <para>
    782               First, make sure to format your Annotation Types following the rules
    783               detailed in
    784               <xref linkend="annotations.bestpractices" />
    785             </para>
    786             <para>
    787               Then, before exporting, it is probably a good idee to run the
     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
    788537              <guilabel>Experiment Overview</guilabel>
    789               detailed in
    790               <xref linkend="experiments_analysis.experiment.overview" />
    791               . By selecting stringent criteria from the interface, the tool will
    792               detect all missing information that could be requested by Repositories
    793             </para>
    794             <para>
    795               Finally, if the Experiment Overview does not report any error any more,
    796               you can run the tab2mage export plugin suitable for ArrayExpress at EBI
    797             </para>
    798           </answer>
    799         </qandaentry>
    800 
    801         <qandaentry>
    802           <question>
    803             <para>
    804               I have exported in Tab2mage file, does it mean I am MIAME compliant ?
    805             </para>
    806           </question>
    807           <answer>
    808             <para>
    809               NO, not necessarily! Tab2mage exporter complies with Tab2mage
    810               specifications so you will be Tab2mage compliant. However, MIAME
     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
    811565              compliance depends very much on the kind of annotation you have
    812566              supplied. Please refer to the previous question for more information
    … …  
    827581          <answer>
    828582            <para>
    829               This is not a good news. In the absence of a data exporter, it is
    830               advised to keep the native datafiles generated by scanners on the file
    831               system and to name RawBioassays with the datafile names associated with
    832               it. This ensures an easy tab2mage export.
    833             </para>
    834           </answer>
    835         </qandaentry>
    836 
    837         <qandaentry>
    838           <question>
    839             <para>
    840               I have created pooled samples in BASE2. Can I export in tab2mage format
    841               ?
    842             </para>
    843           </question>
    844           <answer>
    845             <para>
    846               No, sorry, not for the moment. In its current implementation, BASE2
    847               tab2mage exporter does not support Pooling events. We are working on
    848               adding this features in future version of the plugin. So watch the BASE2
    849               plugin space for upgrades.
     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.
    850604            </para>
    851605          </answer>
    852606        </qandaentry>
    853607      </qandaset>
    854     </sect1>
    855 
    856     <sect1 id="faqs.global.analysis">
     608    </chapter>
     609
     610    <chapter id="faqs.analysis">
    857611      <title>Analysis related FAQs</title>
    858612      <qandaset defaultlabel='qanda'>
    859         <qandaentry>
    860           <question>
    861             <para>
    862               Is it possible to use the FormulaFilter to filter for null fields (or
    863               non null fields)?
    864             </para>
    865           </question>
    866           <answer>
    867             <para></para>
     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>
    868629          </answer>
    869630        </qandaentry>
    … …  
    873634            <para>
    874635              OK, I have uploaded 40 CEL files in BASE2 but are there any tool to
    875               perform normalization on Affymetrix raw data ?
    876             </para>
    877           </question>
    878           <answer>
    879             <para>
    880               Yes, there is. BASE2 team has created a plugin based on
    881               <ulink url="http://rmaexpress.bmbolstad.com/">here</ulink>
    882               RMAExpress methods from Bolstad and Irizarry so you can normalize
     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
    883644              Affymetrix datasets of reasonable size (not 1000 CEL files at a time
    884645              though even though this might depend on your set-up...)
    885             </para>
    886             <para>
    887               Additionnally, thanks to BASE2 web services, you can access BASE2
    888               remotely from R environment running on more powerfull machine for
    889               example. This can give you more flexibility for performing normalization
    890               on large Affymetrix data sets.
    891             </para>
    892             <note>
    893               <para>
    894                 The web service currently only works for Affymetrix raw bioassays
    895               </para>
    896             </note>
     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>
    897650          </answer>
    898651        </qandaentry>
    899652      </qandaset>
    900     </sect1>
    901   </chapter>
     653    </chapter>
    902654</part>
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