title: Empirical null distribution based modeling of multi-class differential gene expression detection.
abstract: In this paper, we study the multi-class differential gene expression detection for microarray data. We propose a likelihood based approach to estimating an empirical null distribution to incorporate gene interactions and provide more accurate false positive control than the commonly used permutation or theoretical null distribution based approach. We propose to rank important genes by p-values or local false discovery rate based on the estimated empirical null distribution. Through simulations and application to a lung transplant microarray data, we illustrate the competitive performance of the proposed method.
authors.affiliation: Division of Biostatistics, School of Public Health, University of Minnesota, Minneapolis, MN, USA.
authors.forename: Xiting
authors.initials: X
authors.lastname: Cao
authors.forename: Baolin
authors.initials: B
authors.lastname: Wu
authors.forename: Marshall I
authors.initials: MI
authors.lastname: Hertz
keywords: Differential expression detection; Empirical Bayes modeling; Empirical null distribution; False discovery rate; Gene expression data
references.citation: Bioinformatics. 2006 Jul 1;22(13):1608-15
references.pmid: 16632494
references.citation: Bioinformatics. 2006 Dec 15;22(24):3025-31
references.pmid: 17046978
references.citation: Biologics. 2008 Dec;2(4):875-84
references.pmid: 19707465
references.citation: Transplant Proc. 2006 Jul-Aug;38(6):1742-3
references.pmid: 16908269
references.citation: J Mol Biol. 2010 Jan 15;395(2):254-69
references.pmid: 19853614
references.citation: Transplantation. 1994 Aug 27;58(4):419-23
references.pmid: 7915442
references.citation: Lab Invest. 2000 Nov;80(11):1643-50
references.pmid: 11092524
references.citation: Ann Transplant. 2008;13(2):54-8
references.pmid: 18566561
references.citation: Mol Cell Biochem. 2008 Apr;311(1-2):57-65
references.pmid: 18165865
references.citation: Stat Appl Genet Mol Biol. 2004;3:Article3
references.pmid: 16646809
references.citation: BMC Bioinformatics. 2009 Mar 16;10:84
references.pmid: 19291295
references.citation: Am J Respir Crit Care Med. 2003 Nov 15;168(10):1237-42
references.pmid: 12958056