articleBioinformaticsJan 28, 2009HYBRID OA

Testing significance relative to a fold-change threshold is a TREAT

DJDavis J. McCarthyGKGordon K. Smyth

Walter and Eliza Hall Institute of Medical Research

PubMed
Indexed incrossrefdoajpubmed

Abstract

MOTIVATION: Statistical methods are used to test for the differential expression of genes in microarray experiments. The most widely used methods successfully test whether the true differential expression is different from zero, but give no assurance that the differences found are large enough to be biologically meaningful. RESULTS: We present a method, t-tests relative to a threshold (TREAT), that allows researchers to test formally the hypothesis (with associated p-values) that the differential expression in a microarray experiment is greater than a given (biologically meaningful) threshold. We have evaluated the method using simulated data, a dataset from a quality control experiment for microarrays and…

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Topics & keywords

Topics
Keywords
  • Bioconductor
  • False discovery rate
  • DNA microarray
  • Multiple comparisons problem
  • Differential (mechanical device)
  • Computer science
  • Data mining
  • Software
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