Version 16 (modified by Jari Häkkinen, 14 years ago) (diff)

Fixed broken link.

Normalization package for BASE

This package contains different kinds of normalization plug-ins, each one implementing a specific algorithm.
The plug-ins in this package require BASE 2.7.0 or later.

Normalization algorithms supported in this package:

  • Average normalization
  • Quantile normalization

More about the plug-ins and their algorithms can be found in the README file.


README contains general information about the plug-ins in this package.
INSTALL contains installation instructions.


The Normalization package for BASE package is an open source project and is available free of charge under the GNU General Public License.


Download the stable normalizers package (MD5).

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 normalizers-devel

or browse the svn repository.


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.


Please use the BASE mailing lists for discussions about the normalization 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.


Assigned tickets:

qQuantiler should select all assays as reference by default
Change qQuantilerNormalization underlying binary to use the new BFS format
Refactor qQuantileNormalizer plugin to use the ExternalProgramExecutor plugin

Open but not assigned tickets:

Create rank invariant normalizer
net.sf.basedb.normalizers: Add proper 2-channel support to qQuantileNormalizer
Request: R/G quantile normalization

All open tickets

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