Illumina plug-ins package for BASE

This package contains plug-ins for the Illumina platform. The plug-ins require BASE 2.9.0 or later and that you have data in the form of either:

• For expression experiments: Illumina Bead Summary (IBS) and Illumina Sentrix® Array binary manifest (BGX) files.
• For SNP experiments: Illumina SNP manifest files in CSV format, Illumina SNP raw data files from BeadStudio.

Expression data plug-ins in this package:

• Background correction: BeadStudio like background correction methods
• Bead summary importer: Import Illumina Bead Summary files as raw bioassay data
• BGX feature importer: Create array designs from BGX files
• BGX reporter importer: Import reporter annotations from BGX files
• Detection P-value calculation: BeadStudio like detection P-value calculations

SNP data plugins in this package:

• SNP reporter importer: Import reporter annotations from SNP manifest files
• SNP raw data importer: Creates raw bioassays from SNP raw data files
• SNP intensity calculator: Extracts data from the raw data files and stores it as a root bioassayset in BASE

Documentation

INSTALL​ describes how to install the plug-in package. It is important that you read this document. The plug-ins require additional raw data tables and reporter annotation columns in the database before they can be used.

README​ contains general information about the plug-ins and specific information for expressions experiments.

README_SNP​ contains specific information for SNP experiments.

README_beadstudio2ibs.txt​ contains information on how to convert Illumina BeadStudio expression projects to a format usable with this package. This read me file and the associated Perl script is not released as a part of a package yet but it is usable with the 1.2 version and the perl script can be downloaded, ​beadstudio2ibs.pl

License

​GNU General Public License version 3.

Download

Version	Revision	Date	Binary (tar.gz)	BASE Version
1.2	912	Dec 10, 2008	illumina-plugins-1.2.tar.gz​ (95kB)	2.9.0 or later
1.1	702	May 23, 2008	illumina-plugins-1.1.tar.gz​ (95kB)	2.6.0 or later
1.0	632	March 13, 2008	illumina-plugins-1.0.tar.gz​ (80kB)	2.6.0 or later

Source code can be downloaded from the subversion repository. Use the following command to get source code for the 1.1 version:

svn co http://baseplugins.thep.lu.se/svn/plugins/base2/net.sf.basedb.illumina/tags/1.1 illumina-1.1

The latest development (maybe unstable; do not use on a production server) revision can be checked out from the repository using the following command:

svn co http://baseplugins.thep.lu.se/svn/plugins/base2/net.sf.basedb.illumina/trunk illumina-devel

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.

Feedback

Please use the ​BASE mailing lists for discussions about the Illumina plug-ins. You have to login to this trac environment to be able to report bugs, enhancement ideas, and feature requests. Login with userid base and password base and use the ​ticket reporting system.

TODO

#463

Illumina expression background correction (version 1.7) does not ask for required permissions to write file