Changeset 4364


Ignore:
Timestamp:
Jul 2, 2008, 9:04:28 AM (15 years ago)
Author:
Nicklas Nordborg
Message:

References #1077: Lowess normalization broken

Added warning in update documentation.

File:
1 edited

Legend:

Unmodified
Added
Removed
  • branches/2.7-stable/doc/src/docbook/admindoc/installation_upgrade.xml

    r4292 r4364  
    6666  <sect1 id="installation_upgrade.upgrade">
    6767    <title>Upgrade instructions</title>
     68
     69    <important id="lowess_bug">
     70      <title>Bug in the LOWESS plug-in affecting BASE version 2.0 -- 2.7.1</title>
     71      <para>
     72      BASE 2.7.2 fixes a serious bug in the LOWESS plug-in. The bug is found in all
     73      BASE versions between 2.0 and 2.7.1, and has caused incorrect normalization values to be
     74      calculated. All data that has been normalized with the LOWESS plug-in prior
     75      to BASE 2.7.2 should be considered invalid and needs to be re-normalized with
     76      the fixed version. Downstream analysis steps that has used the incorrectly
     77      normalized data also needs to be redone. For more information about the bug see
     78      <ulink url="http://base.thep.lu.se/ticket/1077">http://base.thep.lu.se/ticket/1077</ulink>
     79      </para>
     80     
     81      <para>
     82      BASE 2.7.2 includes a utility for finding all experiments/bioassay sets that
     83      includes data normalized with the LOWESS plug-in. An administrator can use
     84      this utility to extract a list of all experiments/bioassay sets that needs to be fixed.
     85      The utility can also tag the name of the found experiments/bioassay sets with
     86      <code>FIX LOWESS</code> to make it easier to find data that needs to be fixed.
     87      </para>
     88     
     89      <para>
     90      The utility can't see any difference between data normalized with the
     91      old version and the fixed version. It will simply report all data that
     92      has been normalized with the LOWESS plug-in. Only use the utility a single
     93      time right after the upgrade to BASE 2.7.2.
     94      </para>
     95     
     96      <para>
     97      The utility is a command line program that should be executed on the web
     98      server.
     99      </para>
     100     
     101      <programlisting>
     102<![CDATA[
     103cd <base-dir>/bin
     104./onetimefix.sh lowess_warn -u <login> -p <password> -f
     105]]>
     106</programlisting>
     107     
     108      <para>
     109        We recommend running the utility as the root user. The <option>-f</option>
     110        option is optional. If it is included the found experiments/bioassay sets
     111        are tagged with <code>FIX LOWESS</code>, otherwise only a list with the
     112        information is generated.
     113      </para>
     114     
     115    </important>
    68116
    69117    <important id="tomcat6">
Note: See TracChangeset for help on using the changeset viewer.