Hunting for significance with the false Discovery rate

Journal of the American Statistical Association

Volumn 104, Issue 486, 2009, Pages 832-840

  Posch, Martin ^a   Zehetmayer, Sonja ^a   Bauer, Peter ^a  

^a MEDICAL UNIVERSITY OF VIENNA   (Austria)

Author keywords

False negative rate; Group sequential tests; Microarray analysis

Indexed keywords

EID: 66549113336     PISSN: 01621459     EISSN: None     Source Type: Journal    
DOI: 10.1198/jasa.2009.0137     Document Type: Article

References (34)

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. (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. Benjamini,Y.,Krieger,A.M., andYekutieli,D. (2006), "Adaptive Linear Step-up Procedures That Control the False Discovery Rate," Biometrika, 93, 491-507.
4. Broberg, P. (2005), "A Comparative Review of Estimates of the Proportion Unchanged Genes and the False Discovery Rate," BMC Bioinformatics, 6, 199-219.
5. Corless, R. M., Jeffrey, D. J., and Knuth, D. E. (1997), "A Sequence of Series for the Lambert W Function," in ISSAC'97, Maui, Hawaii, pp. 197-204.
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. Eaves, I. A., Wicker, L. S., Ghandour, G., Lyons, P. A., Peterson, L. B., Todd, J. A., and Glynne, R. J. (2002), "Combining Mouse Congenic Strains and Microarray Gene Expression Analyses to Study a Complex Trait: The NOD Model of Type 1 Diabetes," Genome Research, 12, 232-243.
8. Efron, B. (2004), "Large-Scale Simultaneous Hypothesis Testing: The Choice of a Null Hypothesis," Journal of the American Statistical Association, 99, 96-104.
9. (2007), "Correlation and Large-Scale Simultaneous Significance Testing," Journal of the American Statistical Association, 102, 93-103.
10. Efron, B., and Tibshirani, R. (2002), "Empirical Bayes Analysis of a Microarray Experiment," Genetic Epidemiology, 23, 70-86.
11. Efron, B., Tibshirani, R., Storey, J., and Tusher, V. (2001), "Empirical Bayes Methods and False Discovery Rates for Microarrays," Journal of the American Statistical Association, 96, 1151-1160.
12. Efron, B., Turnbull, B. B., and Narasimhan, B. (2008), locfdr: Computes Local False Discovery Rates, R Package Version 1.1-6.
13. Finner, H., and Roters, M. (2001), "On the False Discovery Rate and Expected Type I Errors," Biometrical Journal, 43, 985-1005.
14. (2002), "Multiple Hypotheses Testing and Expected Number of Type I Errors," The Annals of Statistics, 30, 220-238.
15. Garber, M. E., Troyanskaya, O. G., Schluens, K., Petersen, S., Thaesler, Z., Pacyna-Gengelbach, M., van de Rijn, M., Rosen, G. D., Perou, C. M., Whyte, R. I., Altman, R., Brown, P. O., Botstein, D., and Petersen, I. (2001), "Diversity of Gene Expression in Adenocarcinoma of the Lung," Proceedings of the National Academy of Sciences of the United States of America, 98, 13784-13789.
16. Genovese, C., and Wasserman, L. (2002), "Operating Characteristics and Extensions of the False Discovery Rate Procedure," Journal of the Royal Statistical Society Series B, 64, 499-517.
17. (2004), "A Stochastic Process Approach to False Discovery Control," The Annals of Statistics, 32, 1035-1061.
18. Jennison, C., and Turnbull, B. W. (2000), Group Sequential Methods with Applications to Clinical Trials, Boca Raton: Chapman & Hall/CRC. Langaas, M., Lindqvist, B. H., and Ferkingstad, E. (2005), "Estimating the Proportion of True Null Hypotheses, With Application to DNA Microarray Data," Journal of the Royal Statistical Society: Series B, 67, 555-572.
19. Mueller, H., Pahl, R., and Schaefer, H. (2007), "Including Sampling and Phenotyping Costs Into the Optimization of Two Stage Designs for Genomewide Association Studies," Genetic Epidemiology, 31, 844-852.
20. Norris, A. W., and Kahn, C. R. (2006), "Analysis of Gene Expression in Pathophysiological States: Balancing False Discovery and False Negative Rates," Proceedings of the National Academy of Sciences of the United States of America, 103, 649-653.
21. Pavlidis, P., Li, Q. H., and Noble, W. (2003), "The Effect of Replication on Gene Expression Microarray Experiments," Bioinformatics (Oxford, England), 19, 1620-1627.
22. Pawitan, Y., Michiels, S., Koscielny, S., Gusnanto, A., and Ploner, A. (2005), "False Discovery Rate, Sensitivity and Sample Size for Microarray Studies," Bioinformatics(Oxford, England), 21, 3017-3024.
23. Pounds, S., and Cheng, C. (2004), "Improving False Discovery Rate Estimation," Bioinformatics (Oxford, England), 20, 1737-1745.
24. R Development Core Team (2005), R: A Language and Environment for Statistical Computing, R Foundation for Statistical Computing, Vienna, Austria, Available at http://www.R-project.org.
25. Ramaswamy, S., Tamayo, P., Rifkin, R., Mukherjee, S., Yeang, C. H., Angelo, M., Ladd, C., Reich, M., Latulippe, E., Mesirov, J. P., Poggio, T., Gerald,W., Loda, M., Lander, E. S., and Golub, T. (2001), "Multiclass Cancer Diagnosis Using Tumor Gene Expression Signatures," Proceedings of the National Academy of Sciences of the United States of America, 98, 15149-15154.
26. Sarkar, S. K. (2004), "FDR-controlling Stepwise Procedures and Their False Negatives Rates," Journal of Statistical Planning and Inference, 125, 119-137.
27. Satagopan, J. M., Verbel, D. A., Venkatraman, E. S., Offit, K. E., and Begg, C. B. (2002), "Two-Stage Designs for Gene-Disease Association Studies," Biometrics, 58, 163-170.
28. Storey, J. D. (2002), "A Direct Approach to False Discovery Rates," Journal of the Royal Statistical Society: Series B, 64, 479-498.
29. 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," Journal of the Royal Statistical Society: Series B, 66, 187-205.
30. Taylor, J., Tibshirani, R., and Efron, B. (2005), "The 'miss rate' for the analysis of gene expression data," Biostatistics (Oxford, England), 6, 111-117.
31. Van den Oord, E. J., and Sullivan, P. F. (2003), "A Framework for Controlling False Discovery Rates and Minimizing the Amount of Genotyping in the Search for Disease Mutations," Human Heredity, 56, 188-199.
32. Victor, A., and Hommel, G. (2007), "Combining Adaptive Designs with Control of the False Discovery Rate - A Generalized Definition for a Global P-value," Biometrical Journal, 49, 94-106.
33. Zehetmayer, S., Bauer, P., and Posch, M. (2005), "Two-Stage Designs for Experiments with a Large Number of Hypotheses," Bioinformatics (Oxford, England), 21, 3771-3777.
34. (2008), "Optimized Multi-stage Designs Controlling the False Discovery or the Family Wise Error Rate," Statistics in Medicine, 27, 4145-4160.