VarMixt: efficient variance modelling for the differential analysis of replicated gene expression data

Bioinformatics
Paul DelmarJean Jacques Daudin

Abstract

Identifying differentially regulated genes in experiments comparing two experimental conditions is often a key step in the microarray data analysis process. Many different approaches and methodological developments have been put forward, yet the question remains open. Varmixt is a powerful and efficient novel methodology for this task. It is based on a flexible and realistic variance modelling strategy. It compares favourably with other popular techniques (standard t-test, SAM and Cyber-T). The relevance of the approach is demonstrated with real-world and simulated datasets. The analysis strategy was successfully applied to both a 'two-colour' cDNA microarray and an Affymetrix Genechip. Strong control of false positive and false negative rates is proven in large simulation studies. The R package is freely available at http://www.inapg.inra.fr/ens_rech/mathinfo/recherche/mathematique/outil.html delmar@inapg.inra.fr http://www.inapg.inra.fr/ens_rech/mathinfo/recherche/mathematique/outil.html.

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Citations

Jul 29, 2011·Applied Microbiology and Biotechnology·Agnès HébertSophie Landaud
Mar 20, 2009·Proceedings of the National Academy of Sciences of the United States of America·Nadéra Mansouri-AttiaJean-Paul Renard
Mar 22, 2012·Microbial Drug Resistance : MDR : Mechanisms, Epidemiology, and Disease·Shaynoor DramsiMichel-Yves Mistou
Dec 21, 2010·Applied and Environmental Microbiology·Marie-Pierre ForquinIsabelle Martin-Verstraete
Dec 12, 2012·Applied and Environmental Microbiology·Agnès HébertJean-Marie Beckerich
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Sep 29, 2006·Journal of Bioinformatics and Computational Biology·Corneliu HenegarJean-Daniel Zucker
Mar 15, 2006·BMC Bioinformatics·Richard J Fox, Matthew W Dimmic
Apr 30, 2008·BMC Bioinformatics·Marie-Laure Martin-MagnietteJean-Jacques Daudin
Feb 15, 2008·BMC Bioinformatics·Tristan Mary-HuardJean-Jacques Daudin
Feb 20, 2010·BMC Microbiology·Sandrine KoechlerPhilippe N Bertin
Jul 29, 2009·International Journal of Radiation Biology·Alexandre PawlikDiana Tronik-Le Roux
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Jan 1, 2014·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Sanghamitra BandyopadhyayAnirban Mukhopadhyay

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