RankProd: a bioconductor package for detecting differentially expressed genes in meta-analysis

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Abstract
Summary: While meta-analysis provides a powerful tool for analyzing microarray experiments by combining data from multiple studies, it presents unique computational challenges. The Bioconductor package RankProd provides a new and intuitive tool for this purpose in detecting differentially expressed genes under two experimental conditions. The package modifies and extends the rank product method proposed by Breitling et al., [(2004)FEBS Lett., 573, 83–92] to integrate multiple microarray studies from different laboratories and/or platforms. It offers several advantages over t-test based methods and accepts pre-processed expression datasets produced from a wide variety of platforms. The significance of the detection is assessed by a non-parametric permutation test, and the associated P-value and false discovery rate (FDR) are included in the output alongside the genes that are detected by user-defined criteria. A visualization plot is provided to view actual expression levels for each gene with estimated significance measurements. Availability: RankProd is available at Bioconductor . A web-based interface will soon be available at Contact:fhong@salk.edu Supplementary information: Supplementary data are available at Bioinformatics online.