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

Bioinformatics. 2006 Nov 15;22(22):2825-7. doi: 10.1093/bioinformatics/btl476. Epub 2006 Sep 18.


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 http://www.bioconductor.org. A web-based interface will soon be available at http://cactus.salk.edu/RankProd

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Computational Biology / methods*
  • DNA, Complementary / metabolism
  • Data Interpretation, Statistical
  • False Positive Reactions
  • Gene Expression Profiling*
  • Gene Expression Regulation
  • Internet
  • Meta-Analysis as Topic*
  • Metabolism
  • Models, Statistical
  • Oligonucleotide Array Sequence Analysis
  • Plant Proteins
  • Proteomics / methods
  • Reproducibility of Results
  • Software


  • DNA, Complementary
  • Plant Proteins