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Bioinformatics. 2017 Sep 1;33(17):2774-2775. doi: 10.1093/bioinformatics/btx292.

RankProd 2.0: a refactored bioconductor package for detecting differentially expressed features in molecular profiling datasets.

Author information

1
Faculty of Science and Engineering, Manchester Institute of Biotechnology, University of Manchester, Manchester M1?7DN, UK.
2
Department of Electrical Engineering and Electronics, University of Liverpool, Liverpool L69?3GJ, UK.
3
Department of Social Science Research Methods, Radboud University Nijmegen, Nijmegen 6525 GD, Netherlands.
4
Institute for Computing and Information Sciences, Radboud University Nijmegen, Nijmegen 6525 EC, Netherlands.
5
Harvard School of Public Health, Dana-Farber Cancer Institute, Boston, MA 02115, USA.

Abstract

Motivation:

The Rank Product (RP) is a statistical technique widely used to detect differentially expressed features in molecular profiling experiments such as transcriptomics, metabolomics and proteomics studies. An implementation of the RP and the closely related Rank Sum (RS) statistics has been available in the RankProd Bioconductor package for several years. However, several recent advances in the understanding of the statistical foundations of the method have made a complete refactoring of the existing package desirable.

Results:

We implemented a completely refactored version of the RankProd package, which provides a more principled implementation of the statistics for unpaired datasets. Moreover, the permutation-based P -value estimation methods have been replaced by exact methods, providing faster and more accurate results.

Availability and implementation:

RankProd 2.0 is available at Bioconductor ( https://www.bioconductor.org/packages/devel/bioc/html/RankProd.html ) and as part of the mzMatch pipeline ( http://www.mzmatch.sourceforge.net ).

Contact:

rainer.breitling@manchester.ac.uk.

Supplementary information:

Supplementary data are available at Bioinformatics online.

PMID:
28481966
PMCID:
PMC5860065
DOI:
10.1093/bioinformatics/btx292
[Indexed for MEDLINE]
Free PMC Article

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