Changeset 276 for trunk/se

Timestamp:

May 21, 2007, 7:44:04 PM (16 years ago)

Author:

Peter Johansson

Message:

updated README for affy package refs #45

File:

• trunk/se/lu/thep/affymetrix/README (modified) (2 diffs)

trunk/se/lu/thep/affymetrix/README

@@ -26 +26 @@
 ----------------------------------------------------------------------
 
-= About se.lu.thep.affymetrix package ===
+= About se.lu.thep.affymetrix package =
 
 Send comments, suggestion, complaints, or questions about this
@@ -41 +41 @@
 
 
-What is RMAExpress plug-in for BASE?
+What is RMAExpress and Plier plug-ins for BASE?
 
-Currently, this is a tool needed to make use of Affymetrix data in
-BASE. Affymetrix data can be imported into BASE as files, but if one
-wants to perform clustering and other analysis available in BASE, the
-data in these files have to be extracted and imported into BASE. There
-may (and probably will) be other ways to analyze Affymetrix data in
-BASE in the future.
+RMAExpress and Plier are two similar plug-ins needed to make use of
+Affymetrix data in BASE. Affymetrix data can be imported into BASE as
+files, but if one wants to perform clustering and other analysis
+available in BASE, the data in these files have to be extracted and
+imported into BASE.
 
-This plug-in do not implement the RMA method itself but rather relies
-on RMAExpressConsole available in the RMAExpress package available at
-http://rmaexpress.bmbolstad.com/. The RMA algorithm is published in
-scientific journals, for more information please refer to the
-RMAExpress web site. In short RMA is the Robust Multichip Average. It
-consists of three steps: a background adjustment, quantile
-normalization, and finally a summarization.
+These plug-ins do not implement the RMA method and Plier method,
+respectively, but rather relies on third-party binary packages.
 
+The RMAExpress plug-in relies on RMAExpressConsole available in the
+RMAExpress package available at http://rmaexpress.bmbolstad.com/. The
+RMA algorithm is published in scientific journals, for more
+information please refer to the RMAExpress web site. In short RMA is
+the Robust Multichip Average. It consists of three steps: a background
+adjustment, quantile normalization, and finally a summarization.
 
-What is required to use the RMAExpress plug-in for BASE? The "BASE
+The Plier plug-in relies on `apt-probeset-summarize` included in
+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`.
+
+What is required to use the these plug-ins for BASE? The "BASE
 getting started document" may also be helpful,
 http://base.thep.lu.se/chrome/site/doc/user/getting_started.html