EEB 518 Notes
Multiple Comparisons: Bonferroni, Sequential Bonferroni Corrections and False Discovery Rates

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  1. lecture notes (pdf file, xx pages)

  2. pdf of recent papers

  1. Allison, D. B., G. L. Gadbury, M. Heo, J. R. Fernandez, C.-K. Lee, T. A. Prolla, and R. Weindruch. 2002. A mixture model approach for the analysis of microarray gene expression data. Computational Statistics and Data Analysis 39: 1-20.
  2. Benjamini, Y., and Hochberg, T. 1995. J. Royal Stat. Soc. B 85: 289--300.
  3. Fernando, R. L., D. Nettleton, B. R. Southey, J. C. M. Dekkers, M. F. Rothschild, and M. Soller. 2004. Controlling the proportion of false positives in multiple dependent tests. Genetics 166: 611-619.
  4. Hochberg, Y. 1988. A sharper Bonferroni procedure for multiple tests of significance. Biometrika 75: 800--802.
  5. Holm, S. 1979. A simple sequential rejective multiple test procedure. Scand. J. Statistics 6: 65--70.
  6. Mosig, M. O., E. Lipkin, G. Khutoreskaya, E. Tchourzyna, M. Soller, and A. Friedmann. 2001 A Whole Genome Scan for Quantitative Trait Loci Affecting Milk Protein Percentage in Israeli-Holstein Cattle, by Means of Selective Milk DNA Pooling in a Daughter Design, Using an Adjusted False Discovery Rate Criterion, Genetics 157: 1683-1698.
  7. Schweder, T. and E. Spjotvoll. 1982. Plots of p-values to evaluate many tests simultaneously. Biometrika 69: 493--502.
  8. Simes, J. R. 1986. An improved Bonferroni procedure for multiple tests of significance. Biometrika 73: 75--754.
  9. Storey J.D. 2002. A direct approach to false discovery rates Journal of the Royal Statistical Society Series B: 64: 479--498.
  10. Storey J.D. 2003. The positive false discovery rate: a Bayesian interpretation and the q-value. Annals of Statistics 31: 2013-2035
  11. Storey JD, Taylor JE, and Siegmund D. 2004 Strong control, conservative point estimation, and simultaneous conservative consistency of false discovery rates: A unified approach. Journal of the Royal Statistical Society, Series B: 66: 187-205.
  12. Storey, J. D., and R. Tibshirani. 2003. Statistical significance for genomewide studies. Proc. Natl. Acad. Sci. 100: 9440--9445.
  13. Thissen, D., L. Steinerg, and D. Kuang. 2002. Quick and easy implementation of the Benjamini-Hochberg procedure for controlling the false positive rate in multiple comparisons. Journal of Educational and Behavioral Statistics 27: 77-83.

  • Software

      • Website for John Storey;s Q-value software for compute q values unfer the pFDR.