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Bioinformatics Advance Access originally published online on March 10, 2009
Bioinformatics 2009 25(9):1203-1204; doi:10.1093/bioinformatics/btp126
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© 2009 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

The tspair package for finding top scoring pair classifiers in R

Jeffrey T. Leek

Department of Oncology, Johns Hopkins School of Medicine, Baltimore, MD 21287, USA


  Abstract

Summary: Top scoring pairs (TSPs) are pairs of genes whose relative rankings can be used to accurately classify individuals into one of two classes. TSPs have two main advantages over many standard classifiers used in gene expression studies: (i) a TSP is based on only two genes, which leads to easily interpretable and inexpensive diagnostic tests and (ii) TSP classifiers are based on gene rankings, so they are more robust to variation in technical factors or normalization than classifiers based on expression levels of individual genes. Here I describe the R package, tspair, which can be used to quickly identify and assess TSP classifiers for gene expression data.

Availability: The R package tspair is freely available from Bioconductor: http://www.bioconductor.org

Contact: jtleek{at}jhu.edu

Associate Editor: Joaquin Dopazo

Received on January 11, 2009; revised on February 16, 2009; accepted on March 1, 2009

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