How accurately can we control the FDR in analyzing microarray data?

Bioinformatics
Sin-Ho Jung, Woncheol Jang

Abstract

We want to evaluate the performance of two FDR-based multiple testing procedures by Benjamini and Hochberg (1995, J. R. Stat. Soc. Ser. B, 57, 289-300) and Storey (2002, J. R. Stat. Soc. Ser. B, 64, 479-498) in analyzing real microarray data. These procedures commonly require independence or weak dependence of the test statistics. However, expression levels of different genes from each array are usually correlated due to coexpressing genes and various sources of errors from experiment-specific and subject-specific conditions that are not adjusted for in data analysis. Because of high dimensionality of microarray data, it is usually impossible to check whether the weak dependence condition is met for a given dataset or not. We propose to generate a large number of test statistics from a simulation model which has asymptotically (in terms of the number of arrays) the same correlation structure as the test statistics that will be calculated from the given data and to investigate how accurately the FDR-based testing procedures control the FDR on the simulated data. Our approach is to directly check the performance of these procedures for a given dataset, rather than to check the weak dependency requirement. We illustrate the propos...Continue Reading

References

Apr 20, 2001·Proceedings of the National Academy of Sciences of the United States of America·V G TusherG Chu
Jul 16, 2002·Nature Medicine·David G BeerSamir Hanash
Oct 6, 2004·Genome Biology·Robert C GentlemanJianhua Zhang
Apr 23, 2005·Bioinformatics·Sin-Ho Jung

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Citations

May 30, 2009·BMC Bioinformatics·Sin-Ho JungPhyllis C Leppert
Jun 30, 2010·BMC Bioinformatics·Omar J JabadoW Ian Lipkin
Feb 27, 2008·BMC Bioinformatics·Kyung In Kim, Mark A van de Wiel
Mar 6, 2012·BMC Genomics·Zhongxue ChenRichard H Scheuermann
Nov 17, 2011·Molecular Biology and Evolution·Fei HeJuliette de Meaux
May 30, 2012·Molecular Biology and Evolution·Fei HeJuliette de Meaux
Aug 6, 2008·Journal of Cellular Physiology·Bradley P CoeWan L Lam
Jan 4, 2012·Clinical and Translational Science·Kouros OwzarSin-Ho Jung
Sep 4, 2012·European Neuropsychopharmacology : the Journal of the European College of Neuropsychopharmacology·Cristina Sánchez-MoraMarta Ribasés
Jan 13, 2015·Cancer Informatics·Sin-Ho Jung, Insuk Sohn
Sep 14, 2006·Physiological Genomics·Tapan S MehtaDavid B Allison
Jun 28, 2007·The Journal of Clinical Endocrinology and Metabolism·Ellen C KaizerPerrin C White

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