title: RankProd: a bioconductor package for detecting differentially expressed genes in meta-analysis.
abstract: 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
authors.affiliation: Plant Biology Laboratory La Jolla, CA, USA. fhong@salk.edu
authors.forename: Fangxin
authors.initials: F
authors.lastname: Hong
authors.forename: Rainer
authors.initials: R
authors.lastname: Breitling
authors.forename: Connor W
authors.initials: CW
authors.lastname: McEntee
authors.forename: Ben S
authors.initials: BS
authors.lastname: Wittner
authors.forename: Jennifer L
authors.initials: JL
authors.lastname: Nemhauser
authors.forename: Joanne
authors.initials: J
authors.lastname: Chory
mesh_terms: 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
chemical_list: D018076:DNA, Complementary; D010940:Plant Proteins