Controlling false discoveries in multidimensional directional decisions, with applications to gene expression data on ordered categories

Biometrics

Volumn 66, Issue 2, 2010, Pages 485-492

  Guo, Wenge ^a   Sarkar, Sanat K ^b   Peddada, Shyamal D ^a  

^a NATIONAL INSTITUTE OF ENVIRONMENTAL HEALTH SCIENCES   (United States)

^b TEMPLE UNIVERSITY   (United States)

Author keywords

Benjamini Hochberg procedure; Directional FDR; Dose response; Microarray; Multiple testing; Ordered categories; Time course

Indexed keywords

CELL CULTURE; STATISTICAL TESTS; STATISTICS;

BENJAMINI-HOCHBERG PROCEDURE; DIRECTIONAL FALSE DISCOVERY RATE; DOSE RESPONSE; FALSE DISCOVERY RATE; GENE EXPRESSION DATA; MULTIPLE TESTING; NULL HYPOTHESIS; ORDERED CATEGORY; TEST STATISTICS; TIME COURSE;

GENE EXPRESSION;

DATA SET; DOSE-RESPONSE RELATIONSHIP; ERROR CORRECTION; GENE EXPRESSION; GENETIC ANALYSIS; HYPOTHESIS TESTING; SIMULATION; TIMESCALE;

ALGORITHM; ARTIFACT; ARTIFICIAL INTELLIGENCE; BIOLOGY; DNA MICROARRAY; GENE EXPRESSION PROFILING; HUMAN; KINETICS; PROCEDURES; SENSITIVITY AND SPECIFICITY; STATISTICS AND NUMERICAL DATA; TIME;

ALGORITHMS; ARTIFACTS; ARTIFICIAL INTELLIGENCE; COMPUTATIONAL BIOLOGY; GENE EXPRESSION PROFILING; HUMANS; KINETICS; METHODS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; SENSITIVITY AND SPECIFICITY; TIME FACTORS;

EID: 77953019375     PISSN: 0006341X     EISSN: 15410420     Source Type: Journal    
DOI: 10.1111/j.1541-0420.2009.01292.x     Document Type: Article

References (20)

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. Benjamini, Y., Hochberg, Y., and Kling, Y. (1993). False discovery rate control in pairwise comparisons. Working paper 93-2
4. Benjamini, Y. and Yekutieli, D. (2005). False discovery rate-adjusted multiple confidence intervals for selected parameters. Journal of the American Statistical Association 100, 71 93.
5. Bernhard, G., Klein, M., and Hommel, G. (2004) Global and multiple test procedures using ordered p-values - A review. Statistical Papers 45, 1 14.
6. Bochkina, N. and Richardson, S. (2007). Tail posterior probability for inference in pairwise and multiclass gene expression data. Biometrics 63, 1117 1125.
7. Finner, H. (1994). Testing multiple hypotheses: General theory, specific problems, and relationships to other multiple decision procedures.
8. Finner, H. (1999). Stepwise multiple test procedures and control of directional errors. Annals of Statistics 27, 274 289.
9. Hommel, G. (1988). A stagewise rejective multiple test procedure based on modified Bonferroni test. Biometrika 75, 383 386.
10. Lin, D., Shkedy, Z., Yekutieli, D., Burzykowski, T., Göhlmann, H., Bondt, A., Perera, T., Geerts, T., and Bijnens, L. (2007). Testing for trends in dose-response microarray experiments: A comparison of several testing procedures, multiplicity and resampling-based inference. Statistical Applications in Genetics and Molecular Biology 6 (1 26.
11. Liu, W. (1996). Control of directional errors with step-up multiple tests. Statistics and Probability Letters 31, 239 242.
12. Lobenhofer, E., Bennett, L., Cable, P., Li, L., Bushel, P., and Afshari, C. (2002). Regulation of DNA replication fork genes by 17 beta-estradiol. Molecular Endocrinology 16, 1215 1229.
13. Peddada, S., Lobenhofer, E., Li, L., Afshari, C., Weinberg, C., and Umbach, D. (2003). Gene selection and clustering for time-course and dose response microarray experiments using order-restricted inference. Bioinformatics 19, 834 841.
14. Sarkar, S. K. and Chang, C.-K. (1997). The Simes method for multiple hypothesis testing with positively dependent test statistics. Journal of the American Statistical Association 92, 1601 1608.
15. Sarkar, S. K., Sen, P. K., and Finner, H. (2004). On two results in multiple testing. In Recent Developments in Multiple Comparisons. IMS Lectures Notes-Monograph Series, 47, Y. Benjamini, F. Bretz, and S. Sarkar (eds 89 99.
16. Shaffer, J. P. (1980). Control of directional errors with stagewise multiple test procedures. Annals of Statistics 8, 1342 1347.
17. Shaffer, J. P. (2002). Multiplicity, directional (type III) errors, and the null hypothesis. Psychological Methods 7, 356 369.
18. Simes, R. J. (1986). An improved Bonferroni procedure for multiple tests of significance. Biometrika 73, 751 754.
19. Tamoto, E., Tada, M., Murakawa, K., Takada, M., Shindo, G., Teramoto, K., Matsunaga, A., Komuro, K., Kanai, M., Kawakami, A., Fujiwara, Y., Kobayashi, N., Shirata, K., Nishimura, N., Okushiba, S., Kondo, S., Hamada, J., Yoshiki, T., Moriuchi, T., and Katoh, H. (2004). Gene-expression profile changes correlated with tumor progression and lymph node metastasis in esophageal cancer. Clinical Cancer Research 10, 3629 3638.
20. Williams, V. S., Jones, V., and Tukey, J. W. (1999). Control errors in multiple comparisons, with examples from state-to-state differences in educational achievement. Journal of Educational and Behavioral Statistics 24, 42 69.