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


BACKGROUND
RankProd is available at Bioconductor http://www.bioconductor.org. A web-based interface will soon be available at http://cactus.salk.edu/RankProd
Hong
Fangxin
F
Plant Biology Laboratory La Jolla, CA, USA. fhong@salk.edu
Breitling
Rainer
R
McEntee
Connor W
CW
Wittner
Ben S
BS
Nemhauser
Jennifer L
JL
Chory
Joanne
J
D019295:Computational Biology / Q000379:methods*; D018076:DNA, Complementary / Q000378:metabolism; D003627:Data Interpretation, Statistical; D005189:False Positive Reactions; D020869:Gene Expression Profiling; D005786:Gene Expression Regulation; D020407:Internet; D015201:Meta-Analysis as Topic; D008660:Metabolism; D015233:Models, Statistical; D020411:Oligonucleotide Array Sequence Analysis; D010940:Plant Proteins; D040901:Proteomics / Q000379:methods; D015203:Reproducibility of Results; D012984:Software
D018076:DNA, Complementary; D010940:Plant Proteins