Choosing the lesser evil: Trade-off between false discovery rate and non-discovery rate

Statistica Sinica

Volumn 18, Issue 3, 2008, Pages 861-879

  Craiu, Radu V ^a   Sun, Lei ^a,b  

^a UNIVERSITY OF TORONTO   (Canada)

^b HOSPITAL FOR SICK CHILDREN RESEARCH INSTITUTE   (Canada)

Author keywords

False discovery rate; Genome scans; Microarray data; Multiple comparisons; Multiple hypothesis testing; Non discovery rate; Power; Type I error; Type II error

Indexed keywords

EID: 55349098276     PISSN: 10170405     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Article

References (26)

1. Benjamini, Y. and Hochberg, Y. (1995). Controlling the false discovery rate: A practical and powerful approach to multiple testing. J. Roy. Statist. Soc. Ser. B 57, 289-300.
2. Benjamini, Y. and Hochberg, Y. (2000). On the adaptive control of the false discovery rate in multiple testing with independent statistics. J. Ed. Behav. Statist. 25, 60-83.
3. Benjamini, Y. and Yekutieli, D. (2001). The control of the false discovery rate in multiple testing under dependency. Amer. Statist. 29, 1165-1188.
4. Black, M. A. (2004). A note on the adaptive control of false discovery rates. J. Roy. Statist. Soc. Ser. B 66, 297-304.
5. Cox, D. R. and Wong, M. Y. (2004). A simple procedure for the selection of significant effects. J. Roy. Statist. Soc. Ser. B 66, 395-400.
6. Delongchamp, R. R., Bowyer, J. F., Chen, J. J. and Kodell, R. L. (2004). Multiple-testing strategy for analyzing cdna array data on gene expression. Biometrics 60, 774-782.
7. Dudoit, S., Shaffer, J. P. and Boldrick, J. C. (2003). Multiple hypothesis testing in microarray experiments. Statist. Sci. 18, 71-103.
8. Efron, B. (2004). Large-scale simultaneous hypothesis testing: the choice of a null hypothesis. J. Amer. Statist. Assoc. 99, 96-104.
9. Efron, B. (2005). Correlation and large-scale simultaneous significance testing. Manuscript Department of Statistics, Stanford University.
10. Finner, H. and Roters, M. (2002). Multiple hypotheses testing and expected number of type I. errors. Ann. Statist. 30, 220-238.
11. Genovese, C. and Wasserman, L. (2001). A large-sample approach to controlling false discovery rates. Tech. Report, Department of Statistics, Carnegie Mellon University.
12. Genovese, C. and Wasserman, L. (2002). Operating characteristics and extensions of the false discovery rate procedure. J. Roy. Statist. Soc. Ser. B 64, 499-517.
13. Langaas, M., Lindqvist, B. H. and Ferkingstad, E. (2005). Estimating the proportion of true null hypotheses, with application to dna microarray data. J. Roy. Statist. Soc. Ser. B 67, 555-572.
14. Li, S. S., Bigler, J., Lampe, J. W., Potter, J. D. and Feng, Z. (2005). Fdr-controlloing testing procedures and sample size determination for microarrays. Statist. Medicine 24, 2267-2280.
15. McPeek, M. S. and Sun, L. (2000). Statistical tests for detection of misspecified relationships by use of genome-screen data. Am. J. Hum. Genet. 66, 1076-1094.
16. Müller, P., Parmigiani, G., Robert, C. and Rousseau, J. (2004). Optimal sample size for multiple testing: the case of gene expression microarrays. J. Amer. Statist. Assoc. 99, 990-1001.
17. Owen, A. B. (2005). Variance of the number of false discoveries. J. Roy. Statist. Soc. Ser. B 67, 411-426.
18. Storey, J. D. (2002). A direct approach to false discovery rates. J. Roy. Statist. Soc. Ser. 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., Taylor, J. E. and Siegmund, D. (2004). Strong control, conservative point estimation and simultaneous conservative consistency of false discovery rates: a unified approach. J. Roy. Statist. Soc. Ser. B 66, 187-205.
21. Storey, J. D. and Tibshirani, R. (2003). Statistical significance for genomewide studies. Proc. Natl. Acad. Sci. USA 100, 9440-9445.
22. Sun, L., Abney, M. and McPeek, M. S. (2001). Detection of misspecified relationships in inbred and outbred pedigrees. Genet. Epidemiol. 21, S36-S41.
23. Sun, L., Craiu, R., Paterson, A. and Bull, S. (2006). Stratified false discovery control for large-scale hypothesis testing with application to genome-wide association studies. Genet. Epidemiol. 30, 519-530.
24. Thomas, D. C., Siemiatycki, J. and Dewar, R. (1985). The problem of multiple inference in studies designed to generate hypotheses. Am. J. Epidemiol. 122, 1080-1095.
25. Tsai, C., Wang, S., Chen, D. and Chen, J. J. (2004). Sample size for gene expression microarray experiments. Bioinformatics 21, 1502-1508.
26. Yekutieli, D. and Benjamini, Y. (1999). Resampling-based false discovery rate controlling multiple test procedures for correlated test statistics. J. Statist. Plann. Inference 82, 171-196.