Mixture models for detecting differentially expressed genes in microarrays.
An important and common problem in microarray experiments is the detection of genes that are differentially expressed in a given number of classes. As this problem concerns the selection of significant genes from a large pool of candidate genes, it needs to be carried out within the framework of multiple hypothesis testing. In this paper, we focus on the use of mixture models to handle the multiplicity issue. With this approach, a measure of the local FDR (false discovery rate) is provided for each gene. An attractive feature of the mixture model approach is that it provides a framework for the estimation of the prior probability that a gene is not differentially expressed, and this probability can subsequently be used in forming a decision rule. The rule can also be formed to take the false negative rate into account. We apply this approach to a well-known publicly available data set on breast cancer, and discuss our findings with reference to other approaches.
Jones
Liat Ben-Tovim
LB
ARC Centre in Bioinformatics, Institute for Molecular Bioscience, University of Queensland, St. Lucia, Brisbane, 4072, Australia. liatj@maths.uq.edu.au
Bean
Richard
R
McLachlan
Geoffrey J
GJ
Zhu
Justin Xi
JX
D000818:Animals; D001943:Breast Neoplasms / Q000235:genetics; D002277:Carcinoma / Q000235:genetics; D018076:DNA, Complementary / Q000032:analysis* / Q000235:genetics; D020869:Gene Expression Profiling / Q000379:methods*; D015972:Gene Expression Regulation, Neoplastic / Q000235:genetics; D006801:Humans; D008954:Models, Biological; D015233:Models, Statistical; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*
D018076:DNA, Complementary