Shrunken p-values for assessing differential expression with applications to genomic data analysis

Biometrics. 2006 Dec;62(4):1099-106. doi: 10.1111/j.1541-0420.2006.00616.x.

Abstract

In many scientific problems involving high-throughput technology, inference must be made involving several hundreds or thousands of hypotheses. Recent attention has focused on how to address the multiple testing issue; much focus has been devoted toward the use of the false discovery rate. In this article, we consider an alternative estimation procedure titled shrunken p-values for assessing differential expression (SPADE). The estimators are motivated by risk considerations from decision theory and lead to a completely new method for adjustment in the multiple testing problem. In addition, the decision-theoretic framework can be used to derive a decision rule for controlling the number of false positive results. Some theoretical results are outlined. The proposed methodology is illustrated using simulation studies and with application to data from a prostate cancer gene expression profiling study.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Biometry
  • Data Interpretation, Statistical
  • Decision Theory
  • Gene Expression Profiling / statistics & numerical data*
  • Genomics / statistics & numerical data*
  • Humans
  • Male
  • Models, Statistical
  • Oligonucleotide Array Sequence Analysis / statistics & numerical data
  • Prostatic Neoplasms / genetics