{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,13]],"date-time":"2026-02-13T09:59:56Z","timestamp":1770976796871,"version":"3.50.1"},"reference-count":32,"publisher":"Oxford University Press (OUP)","issue":"3","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2007,2,1]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Motivation: Inference about differential expression is a typical objective when analyzing gene expression data. Recently, Bayesian hierarchical models have become increasingly popular for this type of problem. The two most common hierarchical models are the hierarchical Gamma\u2013Gamma (GG) and Lognormal\u2013Normal (LNN) models. However, to facilitate inference, some unrealistic assumptions have been made. One such assumption is that of a common coefficient of variation across genes, which can adversely affect the resulting inference.<\/jats:p><jats:p>Results: In this paper, we extend both the GG and LNN modeling frameworks to allow for gene-specific variances and propose EM based algorithms for parameter estimation. The proposed methodology is evaluated on three experimental datasets: one cDNA microarray experiment and two Affymetrix spike-in experiments. The two extended models significantly reduce the false positive rate while keeping a high sensitivity when compared to the originals. Finally, using a simulation study we show that the new frameworks are also more robust to model misspecification.<\/jats:p><jats:p>Availability: The R code for implementing the proposed methodology can be downloaded at<\/jats:p><jats:p>Contact: \u00a0c.lo@stat.ubc.ca<\/jats:p><jats:p>Supplementary information: The supplementary material is available at<\/jats:p>","DOI":"10.1093\/bioinformatics\/btl612","type":"journal-article","created":{"date-parts":[[2006,12,1]],"date-time":"2006-12-01T01:24:12Z","timestamp":1164936252000},"page":"328-335","source":"Crossref","is-referenced-by-count":36,"title":["Flexible empirical Bayes models for differential gene expression"],"prefix":"10.1093","volume":"23","author":[{"given":"Kenneth","family":"Lo","sequence":"first","affiliation":[{"name":"Department of Statistics, University of British Columbia \u00a0 333-6356 Agricultural Road, Vancouver, BC, Canada V6T 1Z2"}]},{"given":"Raphael","family":"Gottardo","sequence":"additional","affiliation":[{"name":"Department of Statistics, University of British Columbia \u00a0 333-6356 Agricultural Road, Vancouver, BC, Canada V6T 1Z2"}]}],"member":"286","published-online":{"date-parts":[[2006,11,30]]},"reference":[{"key":"2023041109381555600_","volume-title":"Affymetrix Microarray Suite User Guide version 5.0","author":"Affymetrix Manual.","year":"2001"},{"key":"2023041109381555600_","doi-asserted-by":"crossref","first-page":"509","DOI":"10.1093\/bioinformatics\/17.6.509","article-title":"A Bayesian framework for the analysis of microarray expression data: regularized t-test and statistical inferences of gene changes","volume":"17","author":"Baldi","year":"2001","journal-title":"Bioinformatics"},{"key":"2023041109381555600_","doi-asserted-by":"crossref","first-page":"630","DOI":"10.1093\/biostatistics\/kxj032","article-title":"A Laplace mixture model for identification of differential expression in microarray experiments","volume":"7","author":"Bhowmick","year":"2006","journal-title":"Biostatistics"},{"key":"2023041109381555600_","doi-asserted-by":"crossref","first-page":"364","DOI":"10.1117\/12.281504","article-title":"Ratio-based decisions and the quantitative analysis of cDNA microarray images","volume":"2","author":"Chen","year":"1997","journal-title":"J. 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