Detecting differential expression in microarray data: comparison of optimal procedures

Background: Many procedures for finding differentially expressed genes in microarray data are based on classical or modified t-statistics. Due to multiple testing considerations, the false discovery rate (FDR) is the key tool for assessing the significance of these test statistics. Two recent papers have generalized two aspects: Storey et al. (2005) have introduced a likelihood ratio test statistic for two-sample situations that has desirable theoretical properties (optimal discovery procedure, ODP), but uses standard FDR assessment; Ploner et al. (2006) have introduced a multivariate local FDR that allows incorporation of standard error information, but uses the standard t-statistic (fdr2d). The relationship and relative performance of these methods in two-sample comparisons is currently unknown. Methods: Using simulated and real datasets, we compare the ODP and fdr2d procedures. We also introduce a new procedure called S2d that combines the ODP test statistic with the extended FDR a...

• Type: Journal
• Year: 2007
• Where: BMCBI
• Authors: Elena Perelman, Alexander Ploner, Stefano Calza, Yudi Pawitan
• Keywords: BMCBI 2007, Procedure, Standard Error Information, Test Statistic