GeneBASE - A tool for estimating gene-level expression from Affymetrix exon arrays

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GeneBASE (Gene-level Background Adjusted Selected probe Expression) is a strategy for estimating gene expression on Affymetrix exon arrays. The method includes a probe-specific background correction and a probe selection strategy in which a subset of probes with highly correlated intensities across multiple samples are chosen to summarize gene exprssion. An extension of the method, GeneBASE-xhyb applies a correction for cross-hybridization biases of gene-level expression.

Program Features
Output gene-level expression indexes | Instructions
Output background-corrected probe intensities | Instructions
Output correlations between probes and off-target transcripts | Instructions
Output presence/absence calls | Instructions


GeneBASE is written by Karen Kapur, from the Wong Lab and Yi Xing. The program uses the following libraries.
GSL - GNU Scientific Library
The C Clustering Library by Michiel Jan Laurens de Hoon


This software is licensed under the GNU General Public License (GPL).

Kapur, K., Jiang, H., Xing, Y. and Wong, W.H. Cross-hybridization modeling on Affymetrix exon arrays. Submitted, 2008.
Kapur, K., Xing, Y., Ouyang, Z. and Wong, W.H. Exon array assessment of gene expression. Genome Biology, 2007 8(5).
Xing, Y., Kapur, K. and Wong, W.H. Probe selection and expression index computation of affymetrix exon arrays. PLoS ONE, 2006, 1(1).

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