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

DOI10.1214/10-STS339MaRDI QIDQ906537zbMATH OpenFDO

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)

Full work available at URL https://arxiv.org/abs/1101.0905, https://projecteuclid.org/euclid.ss/1294167966

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)

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.

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Cites work

• scientific article; zbMATH DE number 3886512 (Why is no real title available?)
• scientific article; zbMATH DE number 720689 (Why is no real title available?)
• scientific article; zbMATH DE number 1750180 (Why is no real title available?)
• A Bayesian Mixture Model for Differential Gene Expression
• A multivariate empirical Bayes statistic for replicated microarray time course data
• Empirical Bayes Analysis of a Microarray Experiment
• Empirical Bayes Microarray ANOVA and Grouping Cell Lines by Equal Expression Levels
• Generalized thresholding estimators for high-dimensional location parameters
• Improved statistical tests for differential gene expression by shrinking variance components estimates
• Linear Models and Empirical Bayes Methods for Assessing Differential Expression in Microarray Experiments
• Microarrays, empirical Bayes and the two-groups model
• On Gene Ranking Using Replicated Microarray Time Course Data
• Operating Characteristics and Extensions of the False Discovery Rate Procedure
• Optimal Threshold from ROC and CAP Curves
• Optimal tests shrinking both means and variances applicable to microarray data analysis
• Saddlepoint Approximations with Applications
• Significance analysis of microarrays applied to the ionizing radiation response

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
• A three-groups model for high-throughput survival screens
• Empirical and fully Bayesian approaches for random effects models in microarray data analysis
• 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

Describes a project that uses

Uses Software

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

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