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Bioinformatics Advance Access published online on November 2, 2005
Bioinformatics, doi:10.1093/bioinformatics/bti750
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© The Author (2005). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org
Received January 14, 2005
Revised August 4, 2005
Accepted October 27, 2005

Article

Using a calibration experiment to assess gene specific information: full Bayesian and empirical Bayesian models for two-channels microarray data

Marta Blangiardo 1*, Simona Toti 1, Betti Giusti 2, Rosanna Abbate 2, Alberto Magi 3, Filippo Poggi 2, Luciana Rossi 2, Francesca Torricelli 4, and Annibale Biggeri 1

1 Dept. of Statistics ‘G.Parenti’, University of Florence & Biostatistic Unit, CSPO, Florence
2 Dept. ‘Area Critica Medico Chirurgica’ University of Florence
3 Dept. ‘Area Critica Medico Chirurgica’ University of Florence; Cytogenetic and Genetic Unit, Careggi Hospital, AOC, Florence
4 Cytogenetic and Genetic Unit, Careggi Hospital, AOC, Florence

* To whom correspondence should be addressed.
Marta Blangiardo, E-mail: m.blangiardo{at}imperial.ac.uk


  Abstract

Motivation: Microarray studies permit to quantify expression levels on a global scale by measuring transcript abundance of thousands of genes simultaneously. A difficulty when analyzing expression measures is how to model variability for the whole set of genes. It is usually unrealistic to assume a common variance for each gene. Several approaches to model gene-specific variances are proposed. We take advantage of calibration experiments, in which the probes hybridized on the two channels come from the same population (self-self experiment). In this case it is possible to estimate the gene-specific variance, to be incorporated in comparative experiments on the same tissue, cellular line or species.

Results: We present two approaches to introduce prior information on gene-specific variability from a calibration experiment: an empirical Bayes model and a full Bayesian hierarchical model. We apply the methods in the analysis of human lipopolysaccharide-stimulated leukocyte experiments.

Availability: The calculations are implemented in WinBugs. The codes are available on request from the authors.


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