se.lu.thep.affymetrix for BASE

This package contains two plug-ins for BASE: RMAExpress and Plier.

RMAExpress and Plier are two similar plug-ins needed to make use of Affymetrix expression chip 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. NOTE, these plug-ins cannot handle snp chip data (see ticket:73).

These plug-ins do not implement the RMA method and Plier method, 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.

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`. For more information regarding the Plier algorithm please refer to the Affymetrix home page.

Documentation

INSTALL​ describes how to install the plug-in (either from a (semi)pre-compiled package or the subversion repository).

README​ contains general information about the plug-in and hints on how to use it.

Information about the underlying algorithms can be found at ​http://rmaexpress.bmbolstad.com/ and ​affymetrix homepage, respectively.

License

​GNU General Public License version 2.

Download se.lu.thep.affymetrix for BASE

Download latest stable release (version 0.7)​ MD5​ (link to source package available below). Works with BASE 2.0 and later.

Subversion Access

The latest stable release can be checked out from the repository using the following command:

svn co https://baseplugins.thep.lu.se/svn/plugins/base2/se.lu.thep.affymetrix/tags/0.7 affymetrix-0.7

The latest development (maybe unstable) revision can be checked out from the repository using the following command:

svn co https://baseplugins.thep.lu.se/svn/plugins/base2/se.lu.thep.affymetrix/trunk affymetrix-devel

or browse the svn repository.

Contribute

After making modifications to the source code, compose a clear and concise log message to describe those changes and the reasons for them. Then, send an email to the developers list containing your log message and the output of svn diff (from the top of your subversion working copy). If the community members consider your changes acceptable, someone who has commit privileges will add your changes to the public source code tree. Recall that permission to directly commit changes to the repository is granted on merit - if you demonstrate comprehension of subversion, programming competency, and a team spirit, you will likely be awarded that permission.

TODO

#43

Add request for proper default permissions (se.lu.thep.affymetrix).

#70

Add releasing procedure to se.lu.thep.affymetrix

#74

unmappable character for encoding UTF8 Copyright (C) Jari Häkkinen (se.lu.thep.affymetrix)

#96

Make the se.lu.thep.affymetrix plug-in compatible with the auto-installation wizard

#169

Running two "New root bioassay set" jobs at the same time makes the second to finish crash