Changeset 4403

Aug 21, 2008, 9:50:55 AM (14 years ago)
Jari Häkkinen

Fixes #925.

2 edited


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

    r4402 r4403  
    3636      <qandaset defaultlabel='qanda'>
    3737        <?dbhtml cellspacing="0px" cellpadding="0px" ?>
    3839        <qandaentry>
    3940          <question>
    8081          </answer>
    8182        </qandaentry>
     84        <qandaentry>
     85          <question>
     86            <simpara>
     87              I get a message "Error: Unable to import root
     88              bioassay. Item not found:
     89              Reporter[externalId=AFFX-2315060]" when i try to create
     90              a root bioassayset.
     91            </simpara>
     92          </question>
     93          <answer>
     94            <simpara>
     95              BASE requires all reporters (probesets in Affymetrix
     96              speak) to be stored in the database before they can be
     97              used. The reporter information is typically imported
     98              from a reporter annotation file but in some cases the
     99              reporter annotation file supplied by Affymetrix fails to
     100              describe all reporters (probesets) on a chip. BASE will
     101              refuse to store data related to such chips until the
     102              missing reporters are added to the database. Hence the
     103              rejection of the new root bioassayset.
     104            </simpara>
     106            <simpara>
     107              The resolution is straightforward, simply import the
     108              probeset information from the CDF file associated with
     109              the array design. The catch is that normal BASE user
     110              credential is not enough to perform the import therefore
     111              someone with proper credential (the BASE server
     112              administrator is one of them) must perform the
     113              import. Follow the instructions at
     114              <xref linkend="reporters.import" /> to import
     115              reporters. Make sure to select plug-in option to ignore
     116              already existing reporters when starting the import
     117              otherwise the existing reporter annotations will be
     118              changed. The goal here is to add missing reporters to
     119              allow BASE work with your data. The CDF file does not
     120              contain any annotation information and cannot be used to
     121              annotate reporters.
     122            </simpara>
     123          </answer>
     124        </qandaentry>
    82126      </qandaset>
    83127    </chapter>
  • trunk/doc/src/docbook/userdoc/reporters.xml

    r3840 r4403  
    88  Copyright (C) 2007 Peter Johansson, Nicklas Nordborg, Philippe Rocca-Serra, Martin Svensson
     9  Copyright (C) 2008 Jari Hakkinen
    1011  This file is part of BASE - BioArray Software Environment.
    171172        web resources.
    172173        </para>
     174        <para>
     175          For some Affymetrix chips the associated CSV file does not
     176          list all reporters on the actual chip. This will lead to
     177          problems in later use of the affected chip types. Simply use
     178          the associated CDF file to import the missing probesets into
     179          BASE, make sure not to upgrade existing reporters when
     180          starting the plug-in. The CDF file contains no annotation
     181          information and consequently annotation information is
     182          removed if the CDF used to upgrade annotations.
     183        </para>
    173184      </note>
    330341        <title>Batch deletion</title>
    331342        <para>
    332           A common problem is to delete reporters that has been accidentaly
     343          A common problem is to delete reporters that has been accidentally
    333344          created. The regular web interface is usually no good since it
    334345          only allows you to select at most 99 reporters at a time. To solve
    413424        </varlistentry>
    414425        <varlistentry>
    415           <term><guilabel>Exernal ID</guilabel></term>
     426          <term><guilabel>External ID</guilabel></term>
    416427          <listitem>
    417428            <para>
    418429            An optional external ID. This value is useful,
    419430            for example, for a tool that automatically
    420             updates the reporter list from som external source.
     431            updates the reporter list from some external source.
    421432            It is not used by BASE.
    422433            </para>
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