Empirical Bayes estimation of genespecific effect

Authors: Jode W Edwards Grier P Page Gary Gadbury Moonseong Heo Tsuyoshi Kayo Richard Weindruch David B Allison

Publish Date: 2004/09/29

Volume: 5, Issue: 1, Pages: 32-39

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Abstract

Microarray technology allows investigators the opportunity to measure expression levels of thousands of genes simultaneously However investigators are also faced with the challenge of simultaneous estimation of gene expression differences for thousands of genes with very small sample sizes Traditional estimators of differences between treatment means ordinary least squares estimators or OLS are not the best estimators if interest is in estimation of gene expression differences for an ensemble of genes In the case that gene expression differences are regarded as exchangeable samples from a common population estimators are available that result in much smaller average meansquare error across the population of gene expression difference estimates We have simulated the application of such an estimator namely an empirical Bayes EB estimator of random effects in a hierarchical linear model normalnormal Simulation results revealed meansquare error as low as 005 times the meansquare error of OLS estimators ie the difference between treatment means We applied the analysis to an example dataset as a demonstration of the shrinkage of EB estimators and of the reduction in meansquare error ie increase in precision associated with EB estimators in this analysis The method described here is available in software that is available at http//wwwsophuabedu/ssgaspid=1087We wish to acknowledge Dr Eva Gropp for her contributions to earlier versions of this manuscript and Dr Alfred Bartolucci for reading two versions of this manuscript and providing many helpful comments This research was supported in part by NSF grants 0217651 and 0090286 NIH grants T32AR007450 P01AG11915 and R01AG18922 an intramural award from the University of Alabama Health Services Foundation and the Frederick Gardner Cottrell Foundation Mention of trade names or commercial products in this article is solely for the purpose of providing specific information and does not imply recommendation or endorsement by the US Department of Agriculture

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