Dataset Information

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

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 Moreover, the permutation-based P -value estimation methods have been replaced by exact methods, providing faster and more accurate results.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.

SUBMITTER: Del Carratore F

PROVIDER: S-EPMC5860065 | biostudies-literature | 2017 Sep

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

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

Del Carratore Francesco F Jankevics Andris A Eisinga Rob R Heskes Tom T Hong Fangxin F Breitling Rainer R

Bioinformatics (Oxford, England) 20170901 17

<h4>Motivation</h4>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 refacto ...[more]

PMID: 28481966

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Dataset Information

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

Motivation

Results

Availability and implementation

Contact

Supplementary information

Publications

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

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