Changeset 4920

May 4, 2009, 11:33:49 AM (13 years ago)
Nicklas Nordborg

Fixes #1120: The dynamic part of BASE should keep track whether intensity data is in log space or not

Updated documentation.

1 edited


  • trunk/doc/src/docbook/appendix/incompatible.xml

    r4844 r4920  
    4444  </note>
     46  <sect1 id="appendix.incompatible.2.12">
     47    <title>BASE 2.12 release</title>
     49    <bridgehead>
     50      Log-2 and log-10 transformed spot intensity data is now allowed
     51    </bridgehead>
     52    <para>
     53      Prior versions of BASE only allowed unlogged spot intensity values.
     54      Analysis plug-ins that operate on spot data should be updated to
     55      check the kind of values that are present in the source bioassay set
     56      and either:
     57    </para>
     58    <itemizedlist>
     59    <listitem>
     60      <para>
     61      Use an appropriate algorithm if it encounters logged data
     62      </para>
     63    </listitem>
     64    <listitem>
     65      <para>
     66      Give an error message that says that it requires unlogged data
     67      </para>
     68    </listitem>
     69    </itemizedlist>
     71    <para>
     72      Plug-ins that are not aware of the type of data may produce unexpected
     73      results if they are applied on logged data. The core plug-ins that are
     74      shipped with BASE has been fixed and they should work with any kind
     75      of data. The <classname>Base1PluginExecuter</classname> that is used
     76      for executing BASE 1 plug-ins can be configured to work with only
     77      a specific kind of data. After upgrading to BASE 2.12 a server admin
     78      should manually update the configuration of all registered BASE 1 plug-ins
     79      with information about what kind of source data that is required and
     80      what kind of result data the plug-in produces. The default setting is that
     81      a plug-in works with any kind of data and produces the same kind of data
     82      used as source.
     83    </para>
     85    <para>
     86      This change also affects formulas, which now has two additional properties:
     87      source and result intensity transform. The source intensity transform property
     88      tells BASE what kind of source data that the formula can be used with. If this
     89      property is not specified the formula can be used with any kind of data. The
     90      result intensity transform property tells BASE what kind of result the forumla
     91      generates. If this property is not specified the formula is expected to
     92      generate the same kind of data as the source data. All existing user-defined
     93      forumlas will not have any of the properties set. After upgrading to BASE 2.12
     94      user should check their formulas and set appropriate values for the source
     95      and result intensity transform attributes.
     96    </para>
     98    <note>
     99      <title>The ch() function automatically converts logged intensities to unlogged</title>
     100      <para>
     101      In order to maintain as much backwards compatibility as possible the ch() function
     102      will automatically convert logged data back to unlogged. This means that many formulas
     103      will continue to work unmodified, but some may create unneccesary complex formulas.
     104      Consider, for example, the log-ratio formula: <code>log2(ch(1) / ch(2))</code>, which
     105      will be converted to: <code>log2(2 ^ rawCh(1) / 2 ^ rawCh(2))</code> if it is applied on
     106      logged values. A better re-write is: <code>rawCh(1) - rawCh(2)</code>.
     107      </para>
     108    </note>
     109  </sect1>
    46111  <sect1 id="appendix.incompatible.2.11">
    47112    <title>BASE 2.11 release</title>
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