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

• Published in: Bioinformatics Vol. 22; no. 22; pp. 2825 - 2827
• Main Authors: Hong, Fangxin, Breitling, Rainer, McEntee, Connor W., Wittner, Ben S., Nemhauser, Jennifer L., Chory, Joanne
• Format: Journal Article
• Language: English
• Published: Oxford Oxford University Press 15.11.2006; Oxford Publishing Limited (England)
• Subjects: Biological and medical sciences; Computational Biology - methods; Data Interpretation, Statistical; DNA, Complementary - metabolism; False Positive Reactions; Fundamental and applied biological sciences. Psychology; Gene Expression Profiling; Gene Expression Regulation; General aspects; Internet; Mathematics in biology. Statistical analysis. Models. Metrology. Data processing in biology (general aspects); Meta-Analysis as Topic; Metabolism; Models, Statistical; Oligonucleotide Array Sequence Analysis; Plant Proteins; Proteomics - methods; Reproducibility of Results; Software; Non parametric test; False positive; Gene; Data acquisition; Statistical model; DNA chip; Rank; Detection; Gene expression; Bioinformatics; Scope note; Metaanalysis
• ISSN: 1367-4803; 1460-2059; 1367-4811
• DOI: 10.1093/bioinformatics/btl476

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.