Empirical Bayes estimation of gene-specific effects in micro-array research

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

Research output: Contribution to journalArticle

6 Citations (Scopus)

Abstract

Micro-array 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 mean-square 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 (normal-normal). Simulation results revealed mean-square error as low as 0.05 times the mean-square error of OLS estimators (i.e., 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 mean-square error, i.e., increase in precision, associated with EB estimators in this analysis. The method described here is available in software that is available at http://www.soph.uab.edu/ssg.asp?id=1087.

Original languageEnglish (US)
Pages (from-to)32-39
Number of pages8
JournalFunctional and Integrative Genomics
Volume5
Issue number1
DOIs
StatePublished - Jan 2005
Externally publishedYes

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Gene Expression
Research
Genes
Research Personnel
Viperidae
Least-Squares Analysis
Sample Size
Population
Linear Models
Software
Technology
Datasets

Keywords

  • Empirical Bayes
  • Estimation
  • Micro-array
  • Shrinkage

ASJC Scopus subject areas

  • Genetics

Cite this

Edwards, J. W., Page, G. P., Gadbury, G., Heo, M., Kayo, T., Weindruch, R., & Allison, D. B. (2005). Empirical Bayes estimation of gene-specific effects in micro-array research. Functional and Integrative Genomics, 5(1), 32-39. https://doi.org/10.1007/s10142-004-0123-0

Empirical Bayes estimation of gene-specific effects in micro-array research. / Edwards, Jode W.; Page, Grier P.; Gadbury, Gary; Heo, Moonseong; Kayo, Tsuyoshi; Weindruch, Richard; Allison, David B.

In: Functional and Integrative Genomics, Vol. 5, No. 1, 01.2005, p. 32-39.

Research output: Contribution to journalArticle

Edwards, JW, Page, GP, Gadbury, G, Heo, M, Kayo, T, Weindruch, R & Allison, DB 2005, 'Empirical Bayes estimation of gene-specific effects in micro-array research', Functional and Integrative Genomics, vol. 5, no. 1, pp. 32-39. https://doi.org/10.1007/s10142-004-0123-0
Edwards, Jode W. ; Page, Grier P. ; Gadbury, Gary ; Heo, Moonseong ; Kayo, Tsuyoshi ; Weindruch, Richard ; Allison, David B. / Empirical Bayes estimation of gene-specific effects in micro-array research. In: Functional and Integrative Genomics. 2005 ; Vol. 5, No. 1. pp. 32-39.
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