Multiple Testing Procedures for the Analysis of Microarray Data

Abstract

We reviewed literature about various multiple testing techniques, especially addressing microarray analyses and small sample sizes, and reanalyzed data from Yuen et al. (Physiological Genomics, 2006) which compared the effect of HgCl2 and Ischemia/Reperfusion injuries on rat kidney tissues. Our analysis uses only 22 rats with small numbers of rats in each treatment group, and 9,501 genes under study. We used empirical Bayes (EB) and permutation testing (implemented in Bioconductor) in an effort to identify differentially expressed genes. EB identified a large number of genes as differentially expressed, including both previously identified and newly identified genes. The newly identified genes appear to have biological functions similar to those previously identified. We also recognized power differences between EB and permutation tests, possibly due to nonnormality of the data but also because permutation tests do not make use of all available information in the data.