A two-sample Bayesian t-test for microarray data

BMC Bioinformatics
Richard J Fox, Matthew W Dimmic

Abstract

Determining whether a gene is differentially expressed in two different samples remains an important statistical problem. Prior work in this area has featured the use of t-tests with pooled estimates of the sample variance based on similarly expressed genes. These methods do not display consistent behavior across the entire range of pooling and can be biased when the prior hyperparameters are specified heuristically. A two-sample Bayesian t-test is proposed for use in determining whether a gene is differentially expressed in two different samples. The test method is an extension of earlier work that made use of point estimates for the variance. The method proposed here explicitly calculates in analytic form the marginal distribution for the difference in the mean expression of two samples, obviating the need for point estimates of the variance without recourse to posterior simulation. The prior distribution involves a single hyperparameter that can be calculated in a statistically rigorous manner, making clear the connection between the prior degrees of freedom and prior variance. The test is easy to understand and implement and application to both real and simulated data shows that the method has equal or greater power compare...Continue Reading

References

Jun 29, 2000·The Journal of Biological Chemistry·S M ArfinG W Hatfield
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
Dec 19, 2001·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·J TheilhaberR Fuchs
Jan 16, 2002·Current Biology : CB·Rachel TompaSteven Henikoff
Jun 6, 2002·Trends in Genetics : TIG·Robert Nadon, Jennifer Shoemaker
Aug 3, 2002·Nature Reviews. Genetics·Yee Hwa Yang, Terry Speed
Aug 10, 2002·Bioinformatics·B P DurbinD M Rocke
Jan 28, 2003·Trends in Genetics : TIG·Jianying Gu, Xun Gu
Apr 16, 2003·Genes & Development·Amir OrianRobert N Eisenman
Apr 19, 2003·Genome Biology·Xiangqin Cui, Gary A Churchill
Aug 19, 2003·Developmental Biology·Noboru SatoAli H Brivanlou
Sep 12, 2003·Bioinformatics·Paul PavlidisWilliam Stafford Noble
Oct 15, 2003·Biostatistics·Raphael GottardoThomas Brettin
Dec 21, 2004·Briefings in Bioinformatics·Jan H Ihmels, Sven Bergmann
Apr 21, 2005·Bioinformatics·Yudi PawitanAlexander Ploner
Jul 17, 2008·Comparative and Functional Genomics·David Philip Kreil, David J C MacKay
Oct 1, 1997·Journal of Biomedical Optics·Y ChenM L Bittner

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Citations

Jan 24, 2008·Proceedings of the National Academy of Sciences of the United States of America·Thomas MockE Virginia Armbrust
Apr 5, 2011·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Hoon KimDimitris Anastassiou
Aug 15, 2009·Briefings in Bioinformatics·Anne-Laure Boulesteix, Martin Slawski
Aug 28, 2007·Bioinformatics·Yvan SaeysPedro Larrañaga
Jul 13, 2011·Antimicrobial Agents and Chemotherapy·Vinod KumarJames R Brown
Aug 2, 2012·Journal of Bioinformatics and Computational Biology·Alok SharmaSatoru Miyano
Jan 8, 2009·BMC Bioinformatics·Jing CaoMichael A White
Feb 12, 2009·BMC Bioinformatics·Eric Yang, Ioannis P Androulakis
Jul 14, 2009·PloS One·Eric H YangIoannis P Androulakis
Aug 2, 2015·BMC Medical Genomics·Henry Han
Mar 2, 2018·International Journal of Molecular Sciences·Tanja ZöllerBjörn Spittau
Jul 31, 2010·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Xiaoxu Han
Oct 9, 2009·The Plant Journal : for Cell and Molecular Biology·José J Reina-PintoAlexander Yephremov
Aug 26, 2010·Journal of Applied Toxicology : JAT·Alexander SuvorovMarie-France Langlois
Sep 14, 2006·Physiological Genomics·Tapan S MehtaDavid B Allison
Aug 8, 2015·Molecular Biology Reports·Esmaeil EbrahimieJagoda Ignjatovic
Mar 12, 2011·Journal of Applied Toxicology : JAT·Alexander Suvorov, Larissa Takser
Oct 22, 2019·Genomics·Konstantina E VennouPantelis G Bagos

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