On permutation procedures for strong control in multiple testing with gene expression data

Statistics and its Interface

Volumn 6, Issue 1, 2013, Pages 79-89

  Rempala, Grzegorz A ^a   Yang, Yuhong ^b  

^a MEDICAL COLLEGE OF GEORGIA   (United States)

^b UNIVERSITY OF MINNESOTA   (United States)

Author keywords

Multiple testing; Permutation test; Step down p value adjustment methods; Strong control of family wise error rate; Subset pivotality property

Indexed keywords

EID: 84876327403     PISSN: 19387989     EISSN: 19387997     Source Type: Journal    
DOI: 10.4310/SII.2013.v6.n1.a8     Document Type: Article

References (18)

1. Bain, L. J. and Engelhardt, M. (1991). Introduction to Probability and Mathematical Statistics, Duxbury Press, North Scituate, MA.
2. Dudoit, S., Shaffer, J. P. and Boldrick, J.C. (2003). Multiple hypothesis testing in microarray experiments. Statistical Science 18(1) 71-103.
3. Dudoit, S. and van der Laan, M. J. (2008). Multiple Testing Procedures with Applications to Genomics. Springer Series in Statistics.
4. Ge, Y., Dudoit, S. and Speed, T. P. (2003). Resampling-based multiple testing for microarray data analysis. TEST 12(1) 1-44 (discussion pp. 44-77).
5. Ge, Y., Sealfon, S. and Speed, T. P. (2009). Multiple testing and its applications to microarrays. Statistical Methods in Medical Research 18(6) 543-563.
6. Hochberg, Y. and Tamhane, A. C. (1987). Multiple Comparison Procedures. John Wiley & Sons, New York.
7. Holm, S. (1979). A simple sequentially rejective multiple test procedure. Scandinavian Journal of Statistics 6 65-70.
8. Hsu, J. C. (1996). Multiple Comparisons. Theory and Methods. Chapman & Hall Ltd, New York.
9. Korn, E. L., Troendle, J. F., McShane, L. M. and Simon, R. (2004). Controlling the number of false discoveries: application to high-dimensional genomic data. Journal of Statistical Planning and Inference 124 379-398.
10. Marcus, R., Peritz, E. and Gabriel, K. R. (1976). On closed testing procedures with special reference to ordered analysis of variance. Biometrika 63 655-660.
11. Kropf, S., Läuter, J., Eszlinger, M., Krohn, K. and Paschke, R. (2004). Nonparametric multiple test procedures with data-driven order of hypotheses and with weighted hypotheses. Journal of Statistical Planning and Inference 125(1) 31-47.
12. Petrondas, D. A. and Gabriel, K. R. (1983). Multiple comparisons by rerandomisation tests. Journal of the American Statistical Association 78 949-957.
13. Pollard, K. and van der Laan, M. (2004). Choice of a null distribution in resampling-based multiple testing Journal of Statistical Planning and Inference 125(1-2) 85-100.
14. Storey, J. D. (2003). The positive false discovery rate: a Bayesian interpretation and the q-value. Annals of Statistics 31(6) 2013-2035.
15. Westfall, P. H. and Young, S. S. (1993). Resampling-based Multiple Testing: Examples and Methods for p-value Adjustment. JohnWiley & Sons, New York.
16. Westfall, P. H. and Wolfinger, R. D. (1997). Multiple tests with discrete distributions. The American Statistician 51 3-8.
17. Westfall, P. H. (2003). Discussion of the paper by Ge, Dudoit and Speed. TEST 12(1) 60-65.
18. Westfall, P. H. and Troendle, J. F. (2008). Multiple testing with minimal assumptions, Biometrical Journal 50 745-755.