The optimal discovery procedure: A new approach to simultaneous significance testing

Journal of the Royal Statistical Society. Series B: Statistical Methodology

Volumn 69, Issue 3, 2007, Pages 347-368

  Storey, John D ^a  

^a UNIVERSITY OF WASHINGTON   (United States)

Author keywords

Classification; False discovery rate; Multiple hypothesis testing; Optimal discovery procedure; Q value; Single thresholding procedure

Indexed keywords

EID: 34249111910     PISSN: 13697412     EISSN: 14679868     Source Type: Journal    
DOI: 10.1111/j.1467-9868.2007.005592.x     Document Type: Article

References (25)

1. Benjamini, Y. Hochberg, Y. (1995) Controlling the false discovery rate: a practical and powerful approach to multiple testing. J. R. Statist. Soc. B, 57, 289 300.
2. Donoho, D. L. Johnstone, I. M. (1995) Adapting to unknown smoothness via wavelet shrinkage. J. Am. Statist. Ass., 90, 1200 1224.
3. Efron, B. Morris, C. N. (1972) Empirical Bayes on vector observations: an empirical Bayes approach. Biometrika, 59, 335 347.
4. Efron, B. Morris, C. N. (1973) Stein's estimation rule and its competitors: an empirical Bayes approach. J. Am. Statist. Ass., 68, 117 130.
5. Efron, B., Tibshirani, R., Storey, J. D. Tusher, V. (2001) Empirical Bayes analysis of a microarray experiment. J. Am. Statist. Ass., 96, 1151 1160.
6. Genovese, C. Wasserman, L. (2002) Operating characteristics and extensions of the false discovery rate procedure. J. R. Statist. Soc. B, 64, 499 517.
7. James, W Stein, C 1961) Estimation with quadratic loss. In Proc. 4th Berkeley Symp. Mathematical Statistics and Probability, vol. 1, pp. 361 379. Berkeley : University of California Press.
8. Lehmann, E. L. (1986) Testing Statistical Hypotheses, 2nd edn. Berlin : Springer.
9. Lehmann, E. L., Romano, J. P. Shaffer, J. P. (2005) On optimality of stepdown and stepup multiple test procedures. Ann. Statist., 33, 1084 1108.
10. Lönnstedt, I. Speed, T. (2002) Replicated microarray data. Statist. Sin., 12, 31 46.
11. Newton, M., Kendziorski, C., Richmond, C., Blatter, F. Tsui, K. (2001) On differential variability of expression ratios: improving statistical inference about gene expression changes from microarray data. J. Computnl Biol., 8, 37 52.
12. Neyman, J. Pearson, E. S. (1933) On the problem of the most efficient tests of statistical hypotheses. Phil. Trans. R. Soc., 231, 289 337.
13. Shaffer, J. (1995) Multiple hypothesis testing. A. Rev. Psychol., 46, 561 584.
14. Soric, B. (1989) Statistical discoveries and effect-size estimation. J. Am. Statist. Ass., 84, 608 610.
15. Spjotvoll, E. (1972) Optimality of some multiple testing procedures. Ann. Math. Statist., 43, 398 411.
16. Stein, C 1956) Inadmissability of the usual estimator for the mean of a multivariate distribution. In Proc. 3rd Berkeley Symp. Mathematical Statistics and Probability, vol. 1, pp. 197 206. Berkeley : University of California Press.
17. Stein, C. (1981) Estimation of the mean of a multivariate Normal distribution. Ann. Statist., 9, 1135 1151.
18. Storey, J. D. (2002) A direct approach to false discovery rates. J. R. Statist. Soc. B, 64, 479 498.
19. Storey, J. D. (2003) The positive false discovery rate: a Bayesian interpretation and the q-value. Ann. Statist., 31, 2013 2035.
20. Storey, J. D 2005 Working Paper 259. Department of Biostatistics, University of Washington, Seattle. (Available from http://www.bepress.com/ uwbiostat/paper259/.)
21. Storey, J. D., Dai, J. Y Leek, J. T 2005 Working Paper 260. Department of Biostatistics, University of Washington, Seattle. (Available from http://www.bepress.com/uwbiostat/paper260/.)
22. Storey, J. D., Dai, J. Y. Leek, J. T. (2006) The optimal discovery procedure for large-scale significance testing, with applications to comparative microarray experiments. Biostatistics, doi: 10.1093/biostatistics/kx1019.
23. Storey, J. D., Taylor, J. E. Siegmund, D. (2004) Strong control, conservative point estimation and simultaneous conservative consistency of false discovery rates: a unified approach. J. R. Statist. Soc. B, 66, 187 205.
24. Storey, J. D. Tibshirani, R. (2003) Statistical significance for genome-wide studies. Proc. Natn. Acad. Sci. USA, 100, 9440 9445.
25. Taylor, J., Tibshirani, R. Efron, B. (2005) The miss rate for the analysis of gene expression data. Biostatistics, 6, 111 117.