Laplace approximated EM microarray analysis: an empirical Bayes approach for comparative microarray experiments

DOI10.1214/10-STS339zbMATH Open1329.62114arXiv1101.0905MaRDI QIDQ906537FDOQ906537

Authors: James G. Booth, Martin T. Wells, Haim Y. Bar, Elizabeth D. Schifano 

Publication date: 22 January 2016

Published in: Statistical Science (Search for Journal in Brave)

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 $imes$ 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.

Full work available at URL: https://arxiv.org/abs/1101.0905

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zbMATH Keywords

EM algorithmLaplace approximationlinear mixed modelsmixture modelempirical Bayesmicroarray analysislocal false discovery ratetwo-groups modelLEMMALIMMA

Mathematics Subject Classification ID

Asymptotic properties of parametric estimators (62F12) Bayesian inference (62F15) Classification and discrimination; cluster analysis (statistical aspects) (62H30) Applications of statistics to biology and medical sciences; meta analysis (62P10) Paired and multiple comparisons; multiple testing (62J15) Design of statistical experiments (62K99)

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Cited In (10)

• Bayesian Classification and Non‐Bayesian Label Estimation via EM Algorithm to Identify Differentially Expressed Genes: a Comparative Study
• Finding causative genes from high-dimensional data: an appraisal of statistical and machine learning approaches
• Robust semiparametric optimal testing procedure for multiple normal means
• Linear mixed model selection for false discovery rate control in microarray data analysis
• lemma
• Empirical and fully Bayesian approaches for random effects models in microarray data analysis
• A three-groups model for high-throughput survival screens
• Evaluation of Laplace distribution-based ANOVA models applied to microarray data
• Differential variation and expression analysis
• A Laplace mixture model for identification of differential expression in microarray experiments

Uses Software

• R
• Bioconductor
• gcrma
• limma
• RankGene
• locfdr

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