Changeset 574 for trunk/se/lu/thep/affymetrix/README

Timestamp:

Feb 7, 2008, 9:54:06 AM (16 years ago)

Author:

Jari Häkkinen

Message:

Added information on how to resolve missing probe set situations.

File:

• trunk/se/lu/thep/affymetrix/README (modified) (1 diff)

trunk/se/lu/thep/affymetrix/README

@@ -189 +189 @@
  6. When the plug-in is finished the resulting expression values will
     be accessible in BASE.
+    [[br]][[br]]
+    In some cases the reporter annotation file from Affymetrix fails
+    to describe all probe sets on the chip, you may get a message like
+    ''Error: Unable to import root bioassay. Item not found:
+    Reporter[externalId=AFFX-2315060]''. In this case you have to fall
+    back to importing the probe set information using the CDF
+    file, simply do 
+    [[br]][[br]]
+    Import the reporters by choosing 'View' -> 'Reporters' and the
+    clicking on 'Import...'. Click 'Next' without changing the 'auto
+    detect' settings. Supply the CDF file name in the next dialog,
+    click 'Next'. Start the import by clicking 'Next' in the parameter
+    dialog. This will add the missing probe sets without changing
+    existing probe sets. The new probe sets will not have any
+    annotations associated with them since the CDFs do not contain
+    such information.
 
  7. You made it here. This means that the plug-in works and you are