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Bioinformatics. 2009 May 1;25(9):1203-4. doi: 10.1093/bioinformatics/btp126. Epub 2009 Mar 10.

The tspair package for finding top scoring pair classifiers in R.

Author information

1
Department of Oncology, Johns Hopkins School of Medicine, Baltimore, MD 21287, USA. jtleek@jhu.edu

Abstract

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.

PMID:
19276151
PMCID:
PMC2672632
DOI:
10.1093/bioinformatics/btp126
[Indexed for MEDLINE]
Free PMC Article
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