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Mixture model on the variance for the differential analysis of gene expression data

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Abstract:

Summary. 

In microarray experiments, accurate estimation of the gene variance is a key step in the identification of differentially expressed genes. Variance models go from the too stringent homoscedastic assumption to the overparameterized model assuming a specific variance for each gene. Between these two extremes there is some room for intermediate models. We propose a method that identifies clusters of genes with equal variance. We use a mixture model on the gene variance distribution. A test statistic for ranking and detecting differentially expressed genes is proposed. The method is illustrated with publicly available complementary deoxyribonucleic acid microarray experiments, an unpublished data set and further simulation studies.

Keywords: Differential analysis; Gene expression; Microarray data; Mixture model; Simulated microarray data; Variance modelling

Document Type: Research Article

DOI: http://dx.doi.org/10.1111/j.1467-9876.2005.00468.x

Affiliations: 1: Laboratoires Fournier, Daix, and Ecole Centrale Paris, Chatenay Malabry, France 2: Institut National de Recherche Agronomique, Paris, France 3: Commisariat de l'Energie Atomique, Evry, France

Publication date: January 1, 2005

bpl/rssc/2005/00000054/00000001/art00003
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