Journal Article

The tspair package for finding top scoring pair classifiers in R

Jeffrey T. Leek

in Bioinformatics

Volume 25, issue 9, pages 1203-1204
Published in print May 2009 | ISSN: 1367-4803
Published online March 2009 | e-ISSN: 1460-2059 | DOI: http://dx.doi.org/10.1093/bioinformatics/btp126

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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@jhu.edu

Journal Article.  1259 words.  Illustrated.

Subjects: Bioinformatics and Computational Biology

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