A multivariate empirical Bayes statistic for replicated microarray time course data

DOI10.1214/009053606000000759MaRDI QIDQ869977zbMATH OpenOpenAlexFDO

Authors Yu Chuan Tai, Terence P. Speed

Publication date 12 March 2007

Published in The Annals of Statistics (Search for Journal in Brave)

Full work available at URL https://arxiv.org/abs/math/0702685

zbMATH Keywords

longitudinalmoderationreplicationgene ranking

Mathematics Subject Classification ID

Time series, auto-correlation, regression, etc. in statistics (GARCH) (62M10) Applications of statistics to biology and medical sciences; meta analysis (62P10) Genetics and epigenetics (92D10) Empirical decision procedures; empirical Bayes procedures (62C12)

Abstract: In this paper we derive one- and two-sample multivariate empirical Bayes statistics (the $mathitMB$-statistics) to rank genes in order of interest from longitudinal replicated developmental microarray time course experiments. We first use conjugate priors to develop our one-sample multivariate empirical Bayes framework for the null hypothesis that the expected temporal profile stays at 0. This leads to our one-sample $mathitMB$-statistic and a one-sample $widetildeT{}^2$-statistic, a variant of the one-sample Hotelling $T^2$-statistic. Both the $mathitMB$-statistic and $widetilde{T}^2$-statistic can be used to rank genes in the order of evidence of nonzero mean, incorporating the correlation structure across time points, moderation and replication. We also derive the corresponding $mathitMB$-statistics and $widetilde{T}^2$-statistics for the one-sample problem where the null hypothesis states that the expected temporal profile is constant, and for the two-sample problem where the null hypothesis is that two expected temporal profiles are the same.

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Cited in

(23)

• On Gene Ranking Using Replicated Microarray Time Course Data
• An empirical Bayes change-point model for transcriptome time-course data
• Regularization method for predicting an ordinal response using longitudinal high-dimensional genomic data
• A hidden spatial-temporal Markov random field model for network-based analysis of time course gene expression data
• Functional Modelling of Microarray Time Series
• Gene profiling for determining pluripotent genes in a time course microarray experiment
• High dimensional extension of the growth curve model and its application in genetics
• A statistical analysis of memory CD8 T cell differentiation: An application of a hierarchical state space model to a short time course microarray experiment
• Finite sample inference for empirical Bayesian methods
• Asymptotic Bayes-optimality under sparsity of some multiple testing procedures
• Laplace approximated EM microarray analysis: an empirical Bayes approach for comparative microarray experiments
• Bayesian feature selection for classification with possibly large number of classes
• Time-course data prediction for repeatedly measured gene expression
• Discovering statistically significant periodic gene expression
• Bayesian growth curve model useful for high-dimensional longitudinal data
• Distance-correlation based gene set analysis in longitudinal studies
• Bayesian models for two-sample time-course microarray experiments
• GAP: a general framework for information pooling in two-sample sparse inference
• Time course analysis of microarray data for the pathway of reproductive development in female rainbow trout
• A multivariate growth curve model for ranking genes in replicated time course microarray data
• A multivariate empirical Bayes statistic for replicated microarray time course data
• Robust semiparametric optimal testing procedure for multiple normal means
• A Markov random field-based approach to characterizing human brain development using spatial-temporal transcriptome data

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