Changeset 4364

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:

• branches/2.7-stable/doc/src/docbook/admindoc/installation_upgrade.xml (modified) (1 diff)

branches/2.7-stable/doc/src/docbook/admindoc/installation_upgrade.xml

@@ -66 +66 @@
   <sect1 id="installation_upgrade.upgrade">
     <title>Upgrade instructions</title>
+
+    <important id="lowess_bug">
+      <title>Bug in the LOWESS plug-in affecting BASE version 2.0 -- 2.7.1</title>
+      <para>
+      BASE 2.7.2 fixes a serious bug in the LOWESS plug-in. The bug is found in all
+      BASE versions between 2.0 and 2.7.1, and has caused incorrect normalization values to be 
+      calculated. All data that has been normalized with the LOWESS plug-in prior 
+      to BASE 2.7.2 should be considered invalid and needs to be re-normalized with
+      the fixed version. Downstream analysis steps that has used the incorrectly
+      normalized data also needs to be redone. For more information about the bug see 
+      <ulink url="http://base.thep.lu.se/ticket/1077">http://base.thep.lu.se/ticket/1077</ulink>
+      </para>
+      
+      <para>
+      BASE 2.7.2 includes a utility for finding all experiments/bioassay sets that
+      includes data normalized with the LOWESS plug-in. An administrator can use
+      this utility to extract a list of all experiments/bioassay sets that needs to be fixed.
+      The utility can also tag the name of the found experiments/bioassay sets with
+      <code>FIX LOWESS</code> to make it easier to find data that needs to be fixed.
+      </para>
+      
+      <para>
+      The utility can't see any difference between data normalized with the 
+      old version and the fixed version. It will simply report all data that
+      has been normalized with the LOWESS plug-in. Only use the utility a single
+      time right after the upgrade to BASE 2.7.2.
+      </para>
+      
+      <para>
+      The utility is a command line program that should be executed on the web
+      server.
+      </para>
+      
+      <programlisting>
+<![CDATA[
+cd <base-dir>/bin
+./onetimefix.sh lowess_warn -u <login> -p <password> -f
+]]>
+</programlisting>
+      
+      <para>
+        We recommend running the utility as the root user. The <option>-f</option>
+        option is optional. If it is included the found experiments/bioassay sets
+        are tagged with <code>FIX LOWESS</code>, otherwise only a list with the
+        information is generated. 
+      </para>
+      
+    </important>
 
     <important id="tomcat6">