Sample size calculations for controlling the distribution of false discovery proportion in microarray experiments

Biostatistics

Volumn 10, Issue 4, 2009, Pages 694-705

  Oura, Tomonori ^a   Matsui, Shigeyuki ^b   Kawakami, Koji ^a  

^a KYOTO UNIVERSITY SCHOOL OF PUBLIC HEALTH   (Japan)

^b INSTITUTE OF STATISTICAL MATHEMATICS   (Japan)

Author keywords

False discovery proportion; Gene expression; Microarray; Sample size

Indexed keywords

ARTICLE; BIOSTATISTICS; DNA MICROARRAY; GENETIC ASSOCIATION; GENETICS; HUMAN; LARGE CELL LYMPHOMA; METHODOLOGY; MORTALITY; NUCLEIC ACID DATABASE; PREDICTIVE VALUE; SAMPLE SIZE; SENSITIVITY AND SPECIFICITY; STATISTICS; SURVIVAL;

BIOSTATISTICS; DATABASES, NUCLEIC ACID; GENOME-WIDE ASSOCIATION STUDY; HUMANS; LYMPHOMA, LARGE B-CELL, DIFFUSE; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PREDICTIVE VALUE OF TESTS; SAMPLE SIZE; SENSITIVITY AND SPECIFICITY; SURVIVAL ANALYSIS;

EID: 74349085386     PISSN: 14654644     EISSN: 14684357     Source Type: Journal    
DOI: 10.1093/biostatistics/kxp024     Document Type: Article

References (22)

1. BENJAMINI, Y. AND HOCHBERG, Y. (1995). Controlling the false discovery rate: a practical and powerful approach to multiple testing. Journal of the Royal Statistical Society, Series 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. Journal of Educational and Behavioral Statistics 25, 60-83.
3. CHOW, S. C., SHAO J. AND WANG H. (2003). Sample Size Calculations in Clinical Research. New York: Marcel Dekker.
4. EFRON, B. (2004). Large-scale simultaneous hypothesis testing: the choice of a null hypothesis. Journal of the American Statistical Association 99, 96-104.
5. GENOVESE, C. R. AND WASSERMAN, L. (2004). A stochastic process approach to false discovery control. The Annals of Statistics 32, 1035-1061.
6. GENOVESE, C. R. AND WASSERMAN, L. (2006). Exceedance control of the false discovery proportion. Journal of the American Statistical Society 101, 1408-1417.
7. JUNG, S. H. (2005). Sample size for FDR-control in microarray data analysis. Bioinformatics 21, 3097-3104.
8. JUNG, S. H., BANG, H. AND YOUNG, S. (2005). Sample size calculation for multiple testing in microarray data analysis. Biostatistics 6, 157-169.
9. KORN, E. L., LI, M. C., MCSHANE, L. M. AND SIMON, R. (2007). An investigation of two multivariate permutation methods for controlling the false discovery proportion. Statistics in Medicine 26, 4428-4440.
10. 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.
11. MATSUI, S., ZENG, S., YAMANAKA, T. AND SHAUGHNESSY, J. (2008). Sample size calculations based on ranking and selection in microarray experiments. Biometrics 64, 217-226.
12. MILLIGAN, G. W. AND COOPER, M. C. (1985). An examination of procedures for determining the number of clusters in a data set. Psychometrika 50, 159-179.
13. PAWITAN, Y., CALZA, S. AND PLONER, A. (2006). Estimation of false discovery proportion under general dependence. Bioinformatics 22, 3025-3031.
14. PAWITAN, Y., MICHIELS, S., KOSCIELNY, S., GUSNANTO, A. AND PLONER, A. (2005). False discovery rate, sensitivity and sample size for microarray studies. Bioinformatics 21, 3017-3024. (Pubitemid 40916427)
15. ROSENWALD, A., WRIGHT, G., CHAN, W. C., CONNORS, J. M., CAMPO, E., FISHER, R. I., GASCOYNE, R. D., MULLER-HERMELINK, H. K., SMELAND, E. B., STAUDT, L. M. and others (2002). The use of molecular profiling to predict survival after chemotherapy for diffuse large B-cell lymphoma. The New England Journal of Medicine 346, 1937-1947.
16. SCHWEDER, T. AND SPJTVOLL, E. (1982). Plots of p-values to evaluate many tests simultaneously. Biometrika 69, 493-502.
17. SHAO, Y. AND TSENG, C. H. (2007). Sample size calculation with dependence adjustment for FDR-control in microarray studies. Statistics in Medicine 26, 4219-4237.
18. STOREY, J. D. (2002). A direct approach to false discovery rates. Journal of the Royal Statistical Society, Series B 64, 479-498.
19. STOREY, J. D. AND TIBSHIRANI, R. (2003). Statistical significance for genomewide studies. Proceedings of the National Academy of Sciences of the United States of America 100, 9440-9445.
20. TSAI, C. A., HSUEH H. M. AND CHEN, J. J. (2003). Estimation of false discovery rates in multiple testing: application to gene microarray data. Biometrics 59, 1071-1081.
21. TSAI, C. A., WANG, S. J., CHEN, D. T. AND CHEN, J. J. (2005). Sample size for gene expression microarray experiments. Bioinformatics 21, 1502-1508.
22. WILLIAMS, D. A. (1975). The analysis of binary responses from toxicological experiments involving reproduction and teratogenicity. Biometrics 31, 949-952.