A multivariate empirical Bayes statistic for replicated microarray time course data

DOI10.1214/009053606000000759zbMATH Open1106.62008arXivmath/0702685OpenAlexW3104024536MaRDI QIDQ869977FDOQ869977

Authors: Yu Chuan Tai, Terence P. Speed 

Publication date: 12 March 2007

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

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.

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

Recommendations

• On Gene Ranking Using Replicated Microarray Time Course Data
• A multivariate growth curve model for ranking genes in replicated time course microarray data
• Linear Models and Empirical Bayes Methods for Assessing Differential Expression in Microarray Experiments
• scientific article; zbMATH DE number 1750180
• Empirical Bayes Analysis of a Microarray Experiment

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)

Cites Work

• Title not available (Why is that?)
• Title not available (Why is that?)
• Comparison of Discrimination Methods for the Classification of Tumors Using Gene Expression Data
• Title not available (Why is that?)
• Comparing the continuous representation of time-series expression profiles to identify differentially expressed genes
• Title not available (Why is that?)
• Title not available (Why is that?)
• Empirical Bayes Analysis of a Microarray Experiment
• Title not available (Why is that?)
• Significance analysis of microarrays applied to the ionizing radiation response
• Title not available (Why is that?)
• Linear Models and Empirical Bayes Methods for Assessing Differential Expression in Microarray Experiments
• Title not available (Why is that?)
• A multivariate empirical Bayes statistic for replicated microarray time course data
• Hidden Markov Models for Microarray Time Course Data in Multiple Biological Conditions
• Functional Hierarchical Models for Identifying Genes with Different Time‐Course Expression Profiles

Cited In (23)

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

Uses Software

• sma

This page was built for publication: A multivariate empirical Bayes statistic for replicated microarray time course data

Report a bug (only for logged in users!)Click here to report a bug for this page (MaRDI item Q869977)