Changes between Initial Version and Version 1 of

May 22, 2007, 9:38:29 AM (15 years ago)
Peter Johansson




    v1 v1  
     1= for BASE =
     3This package contains two plug-ins for BASE: RMAExpress and Plier.
     5RMAExpress and Plier are two similar plug-ins needed to make use of
     6Affymetrix data in BASE. Affymetrix data can be imported into BASE as
     7files, but if one wants to perform clustering and other analysis
     8available in BASE, the data in these files have to be extracted and
     9imported into BASE.
     11These plug-ins do not implement the RMA method and Plier method,
     12but rather relies on third-party binary packages.
     14The RMAExpress plug-in relies on RMAExpressConsole available in the
     15RMAExpress package available at The
     16RMA algorithm is published in scientific journals, for more
     17information please refer to the RMAExpress web site. In short RMA is
     18the Robust Multichip Average. It consists of three steps: a background
     19adjustment, quantile normalization, and finally a summarization.
     21The Plier plug-in relies on `apt-probeset-summarize` included in
     22Affymetrix Power Tools (APT) available at
     24`apt-probeset-summarize` provides several methods (see Affymetrix home
     25page). Here we use the method given with option flag `--option
     26plier-mm`. For more information regarding the Plier algorithm please
     27refer to the Affymetrix home page.
     30= Documentation =
     32[source:trunk/se/lu/thep/affymetrix/INSTALL INSTALL] describes how to install the plug-in (either from a (semi)pre-compiled package or the subversion repository).
     34[source:trunk/se/lu/thep/affymetrix/README README] contains general information about the plug-in and hints on how to use it.
     36Information about the underlying algorithms can be found at and [ affymetrix homepage], respectively.
     39= License =
     41[ GNU General Public License version 2].
     43= Download for BASE =
     45Browse the source source:trunk/se/lu/thep/affymetrix or download latest stable release (soon to come). Works with BASE 2.0 and later.