Version 10 (modified by 17 years ago) ( diff ) | ,
---|
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 http://lev.thep.lu.se/repository/baseplugins/tags/se/lu/thep/affymetrix/0.7 affymetrix-0.7
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
Attachments (8)
- base_affymetrix_plugin-0.6.tar.gz (31.4 KB ) - added by 17 years ago.
- base_affymetrix_plugin-0.6.tar.gz.MD5 (68 bytes ) - added by 17 years ago.
- base_affymetrix_plugin-0.6-src.tar.gz (19.4 KB ) - added by 17 years ago.
- base_affymetrix_plugin-0.6-src.tar.gz.MD5 (72 bytes ) - added by 17 years ago.
- base_affymetrix_plugin-0.7.tar.gz (30.5 KB ) - added by 17 years ago.
- base_affymetrix_plugin-0.7.tar.gz.MD5 (68 bytes ) - added by 17 years ago.
- base_affymetrix_plugin-0.7-src.tar.gz (20.5 KB ) - added by 17 years ago.
- base_affymetrix_plugin-0.7-src.tar.gz.MD5 (72 bytes ) - added by 17 years ago.
Download all attachments as: .zip