Changeset 4131 for trunk/doc/src/docbook/appendix/incompatible.xml

Timestamp:

Feb 8, 2008, 9:55:48 AM (16 years ago)

Author:

Nicklas Nordborg

Message:

Fixes #868: Support for chips with multiple arrays

File:

• trunk/doc/src/docbook/appendix/incompatible.xml (modified) (1 diff)

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

@@ -105 +105 @@
       since this is a new option. In most cases, it should be handled in the same way
       as if the job is <constant>EXECUTING</constant>.
+    </para>
+    
+    <bridgehead>Hybridization to Labeled extracts link</bridgehead>
+    <para>
+      This link can now hold information about which sub-array a labeled
+      extract belongs to on a multi-array hybridization. Code that is
+      unaware of the concept of sub-arrays may find hybridizations 
+      where the number of labeled extracts doesn't match the number
+      channels in the platform used, and that more than one labeled
+      extract has the same label. This was previously considered as
+      an error condition by the experiment validator. With the
+      new scheme the validation has to be done on a sub-array basis instead
+      of on the complete hybridization.
+    </para>
+    
+    <para>
+      A similar issue arises when inheriting annotations to a raw bioassay
+      which stems from a specific sub-array on a mutli-array hybridization.
+      This raw bioassay should only inherit annotations from the labeled
+      extracts that are part of the same sub-array. For API compatibility
+      reasons the <methodname>Hybridization.getAnnotatableParents()</methodname>
+      will still return <emphasis>all</emphasis> labeled extracts. Code
+      that is calling this method in order to find the parents to
+      a raw bioassay should instead call the new method,
+      <methodname>Hybridizations.getAnnotatableParents(int)</methodname>,
+      where the <code>int</code> is the sub-array index value for
+      the raw bioassay.
     </para>