Changeset 293 for trunk/se/lu/thep/affymetrix/README

Timestamp:

May 23, 2007, 2:31:46 PM (16 years ago)

Author:

Peter Johansson

Message:

improved text on PLIER

File:

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

trunk/se/lu/thep/affymetrix/README

@@ -73 +73 @@
 Affymetrix Power Tools (APT) available at
 http://www.affymetrix.com/support/developer/powertools/index.affx.
-`apt-probeset-summarize` provides several methods (see Affymetrix home
-page). Here we use the method given with option flag `--option
-plier-mm`. For more information regarding the Plier algorithm please
-refer to the Affymetrix home page.
+`apt-probeset-summarize` provides several methods and options. For
+time being there is no way to to set these options through the BASE
+GUI. The option `plier-mm` is hard-coded into the plug-in, which
+should be good choice in most situations. In short the option means
+mismatch probe is used as adjustment for perfect match, quantile
+normalization is done, and PLIER is used for summarizing probesets.
+For more information regarding the PLIER algorithm please refer to the
+Affymetrix home page.