Resampling-based multiple testing for microarray data analysis

Yongchao Ge, Sandrine Dudoit, Terence P. Speed, Gary Glonek, Patty Solomon, Gregory R. Grant, Christina M. Kendziorski, John H. Maindonald, John D. Storey, Peter H. Westfall

Research output: Contribution to journalReview article

342 Scopus citations

Abstract

The burgeoning field of genomics has revived interest in multiple testing procedures by raising new methodological and computational challenges. For example, microarray experiments generate large multiplicity problems in which thousands of hypotheses are tested simultaneously. Westfall and Young (1993) propose resampling-based p-value adjustment procedures which are highly relevant to microarray experiments. This article discusses different criteria for error control in resampling-based multiple testing, including (a) the family wise error rate of Westfall and Young (1993) and (b) the false discovery rate developed by Benjamini and Hochberg (1995), both from a frequentist viewpoint; and (c) the positive false discovery rate of Storey (2002a), which has a Bayesian motivation. We also introduce our recently developed fast algorithm for implementing the minP adjustment to control family-wise error rate. Adjusted p-values for different approaches are applied to gene expression data from two recently published microarray studies. The properties of these procedures for multiple testing are compared.

Original languageEnglish (US)
Pages (from-to)1-77
Number of pages77
JournalTest
Volume12
Issue number1
DOIs
StatePublished - Jun 2003

All Science Journal Classification (ASJC) codes

  • Statistics and Probability
  • Statistics, Probability and Uncertainty

Keywords

  • Adjusted p-value
  • False discovery rate
  • Family-wise error rate
  • Fast algorithm
  • Microarray
  • MinP
  • Multiple testing

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  • Cite this

    Ge, Y., Dudoit, S., Speed, T. P., Glonek, G., Solomon, P., Grant, G. R., Kendziorski, C. M., Maindonald, J. H., Storey, J. D., & Westfall, P. H. (2003). Resampling-based multiple testing for microarray data analysis. Test, 12(1), 1-77. https://doi.org/10.1007/BF02595811