Microarray Softwares

BooleanNet

Introduction

This program was used to create Boolean implication network [ 1 ].

Releases

• BooleanNetTest.tar.gz [ Released 07-16-2011 ]
  License: GPL

Documentation

tar xvzf BooleanNetTest.tar.gz
cd BooleanNetTest
bash scr

Memory efficient RMA

Introduction

This version of RMA uses disk and memory efficiently to normalize thousands of Affymetrix gene expression data together. It is a modification of the RMA software released from the SRC public software repository ( http://morden.csee.usf.edu/software .) Thanks to SRC for distributing this open source system.

We modified the software to normalize large sets of Affymetrix gene expression arrays as part of the process of building Boolean implication networks [ 1 ], a genomic network representation that we have used to discover developmentally regulated genes in hematopoiesis [ 2 , 3 ].

The purpose of the project was not to produce new array normalization software. While the software works for us, it is not written to be "industrial strength", it may be fragile and/or buggy. Feel free to contact us if you need help, but we can only offer very limited help.

It is distributed under the GNU Public License (GPL), so feel free to make your own modifications and improvements as well.

Releases

• rma-1.0.tar.gz [ Released 06-22-2010 ]
  License: GPL

Contact

• Debashis Sahoo
• David Dill

Documentation

tar xvzf rma-1.0.tar.gz
cd USF-softwares
bash scr

RMA=affy-apps/rma/rma
rm -f tmpint tmpint.mean
$RMA -o expr-local.txt -s tmpint -c path_to_cdf_dir `cat filelist`
$RMA -o expr.txt -c path_to_cdf_dir --combine=tmpint-list

filelist

List of CEL files.

path_to_cdf_dir

A directory with the required CDF files for normalization.

tmpint

Name of the file used to store intermediate computation results.

tmpint-list

A list of temporary intermediate files that are created by passing -s tmpint command-line argument.

sample tmpint-list:

./tmpint