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Bioinformatics Advance Access published online on May 7, 2007
Bioinformatics, doi:10.1093/bioinformatics/btm159
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© The Author (2007). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

CALIB: a Bioconductor package for estimating absolute expression levels from two-color microarray data

Hui Zhao 1, Kristof Engelen 1, Bart De Moor 2 and Kathleen Marchal 1,2,*

1 CMPG-BioI, Department of Microbial and Molecular Systems, K.U.Leuven, Kasteelpark Arenberg 20, B-3001 Leuven-Hevelee, Belgium
2 BIOI@SCD, Department of Electrical Engineering (ESAT), K.U.Leuven, Kasteelpark Arenberg 10, B-3001 Leuven-Hevelee, Belgium

*To whom correspondence should be addressed. Prof. Kathleen Marchal, E-mail: kathleen.marchal{at}biw.kuleuven.be


  Abstract

In this paper we describe a new Bioconductor package "CALIB" for normalization of two-color microarray data. This approach is based on the measurements of external controls and estimates an absolute target level for each gene and condition pair, as opposed to working with log-ratios as a relative measure of expression. Moreover, this method makes no assumptions regarding the distribution of gene expression divergence.

Availability: http://bioconductor.org/packages/2.0/bioc Open Source

Associate Editor: Dr. Joaquin Dopazo

Received on March 15, 2007; revised on April 16, 2007; accepted on April 18, 2007

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