A simple implementation of a normal mixture approach to differential gene expression in multiclass microarrays

Bioinformatics
G J McLachlanL Ben-Tovim Jones

Abstract

An important problem in microarray experiments is the detection of genes that are differentially expressed in a given number of classes. We provide a straightforward and easily implemented method for estimating the posterior probability that an individual gene is null. The problem can be expressed in a two-component mixture framework, using an empirical Bayes approach. Current methods of implementing this approach either have some limitations due to the minimal assumptions made or with more specific assumptions are computationally intensive. By converting to a z-score the value of the test statistic used to test the significance of each gene, we propose a simple two-component normal mixture that models adequately the distribution of this score. The usefulness of our approach is demonstrated on three real datasets.

References

Jun 9, 1999·Proceedings of the National Academy of Sciences of the United States of America·U AlonA J Levine
Aug 30, 2000·Proceedings of the National Academy of Sciences of the United States of America·M L LeeJ Sklar
Feb 24, 2001·The New England Journal of Medicine·I HedenfalkG Sauter
Apr 20, 2001·Proceedings of the National Academy of Sciences of the United States of America·V G TusherG Chu
May 8, 2001·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·M A NewtonK W Tsui
Jul 12, 2002·Genetic Epidemiology·Bradley Efron, Robert Tibshirani
Jul 29, 2003·Proceedings of the National Academy of Sciences of the United States of America·John D Storey, Robert Tibshirani
Apr 21, 2005·Bioinformatics·Yudi PawitanAlexander Ploner
Aug 4, 2005·Journal of Bioinformatics and Computational Biology·Xu Guo, Wei Pan
Dec 22, 2005·Bioinformatics·Alexander PlonerYudi Pawitan
Mar 1, 1942·Proceedings of the National Academy of Sciences of the United States of America·E B Wilson

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Citations

Jan 23, 2008·Functional & Integrative Genomics·Shuo Jiao, Shunpu Zhang
Jul 23, 2004·Nature·Michael MorleyVivian G Cheung
Mar 30, 2013·Journal of Applied Statistics·Xiting CaoMarshall I Hertz
Aug 31, 2010·Bioinformatics·Paul D McNicholas, Thomas Brendan Murphy
Jul 11, 2008·BMC Bioinformatics·Korbinian Strimmer
Aug 19, 2007·BMC Developmental Biology·Sigrid A LehnertPaul L Greenwood
May 10, 2008·BMC Proceedings·Cyril DalmassoPhilippe Broët
Jan 6, 2007·Genome Biology·Guang ChenChristian J Stoeckert
Oct 20, 2011·Genome Biology·Florence M G CavalliNicholas M Luscombe
May 5, 2009·PLoS Computational Biology·Nicholas J HudsonBrian P Dalrymple
Jan 1, 2008·The International Journal of Biostatistics·Weiliang QiuRoss Lazarus
May 22, 2013·Computational and Mathematical Methods in Medicine·Hisashi Noma, Shigeyuki Matsui
Dec 10, 2013·Bioinformatics·Hongjie Zhu, Man Luo
Jan 30, 2014·BMC Systems Biology·Aaron B InghamNicholas J Hudson
Dec 17, 2009·Artificial Intelligence in Medicine·Mingyi Wang, Jake Y Chen
Nov 21, 2009·European Journal of Cancer : Official Journal for European Organization for Research and Treatment of Cancer (EORTC) [and] European Association for Cancer Research (EACR)·Liangdan TangShu-Wing Ng
Feb 18, 2010·Computational Statistics & Data Analysis·Abbas KhaliliShili Lin
Feb 18, 2010·Computational Statistics & Data Analysis·W M MuirJ Ogas
Oct 29, 2015·Biomarkers in Medicine·James J ChenWei-Jiun Lin
Apr 11, 2009·Statistics in Medicine·Ismaïl AhmedPascale Tubert-Bitter
Jan 1, 2010·Journal of the Royal Statistical Society. Series C, Applied Statistics·Peng Wei, Wei Pan
May 13, 2014·IEEE Transactions on Medical Imaging·Hien D NguyenAndrew L Janke
May 22, 2013·Computational and Mathematical Methods in Medicine·Keita MoriShigeyuki Matsui
Oct 24, 2007·Journal of Biomedical Informatics·Pritha Mahata, Kaushik Mahata

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