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August 2010 Laplace Approximated EM Microarray Analysis: An Empirical Bayes Approach for Comparative Microarray Experiments
Haim Bar, James Booth, Elizabeth Schifano, Martin T. Wells
Statist. Sci. 25(3): 388-407 (August 2010). DOI: 10.1214/10-STS339

Abstract

A two-groups mixed-effects model for the comparison of (normalized) microarray data from two treatment groups is considered. Most competing parametric methods that have appeared in the literature are obtained as special cases or by minor modification of the proposed model. Approximate maximum likelihood fitting is accomplished via a fast and scalable algorithm, which we call LEMMA (Laplace approximated EM Microarray Analysis). The posterior odds of treatment × gene interactions, derived from the model, involve shrinkage estimates of both the interactions and of the gene specific error variances. Genes are classified as being associated with treatment based on the posterior odds and the local false discovery rate (f.d.r.) with a fixed cutoff. Our model-based approach also allows one to declare the non-null status of a gene by controlling the false discovery rate (FDR). It is shown in a detailed simulation study that the approach outperforms well-known competitors. We also apply the proposed methodology to two previously analyzed microarray examples. Extensions of the proposed method to paired treatments and multiple treatments are also discussed.

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Haim Bar. James Booth. Elizabeth Schifano. Martin T. Wells. "Laplace Approximated EM Microarray Analysis: An Empirical Bayes Approach for Comparative Microarray Experiments." Statist. Sci. 25 (3) 388 - 407, August 2010. https://doi.org/10.1214/10-STS339

Information

Published: August 2010
First available in Project Euclid: 4 January 2011

zbMATH: 1329.62114
MathSciNet: MR2791674
Digital Object Identifier: 10.1214/10-STS339

Rights: Copyright © 2010 Institute of Mathematical Statistics

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Vol.25 • No. 3 • August 2010
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