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Selecting Multiple Biomarker Subsets with Similarly Effective Binary Classification Performances
07:35

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Published on: October 11, 2018

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

Jeffrey T Leek1

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

Bioinformatics (Oxford, England)
|March 12, 2009
PubMed
Summary
This summary is machine-generated.

Top scoring pairs (TSPs) offer a robust and cost-effective method for classifying individuals using gene expression data. The new R package, tspair, simplifies the identification and assessment of these powerful gene-based diagnostic tools.

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • Top scoring pairs (TSPs) are gene pairs that accurately classify individuals based on relative gene rankings.
  • TSPs offer advantages in interpretability, cost-effectiveness, and robustness against technical variations compared to standard gene expression classifiers.

Purpose of the Study:

  • To introduce the R package, tspair, for identifying and evaluating Top Scoring Pair (TSP) classifiers.
  • To provide a tool for researchers working with gene expression data.

Main Methods:

  • The study describes the functionality of the R package, tspair.
  • The package utilizes gene ranking for classification, enhancing robustness.

Main Results:

  • The tspair package enables quick identification and assessment of TSP classifiers.
  • TSP-based classification is shown to be robust to technical variations and normalization.

Conclusions:

  • The tspair R package is a valuable tool for leveraging Top Scoring Pairs in gene expression analysis.
  • This approach facilitates the development of simple, inexpensive, and reliable diagnostic tests based on gene expression patterns.