Testing the disjunction hypothesis using Voronoi diagrams with applications to genetics

Annals of Applied Statistics

Volumn 8, Issue 2, 2014, Pages 801-823

  Phillips, Daisy ^a   Ghosh, Debashis ^a  

^a PENNSYLVANIA STATE UNIVERSITY   (United States)

Author keywords

Empirical null distributions; False discovery rates; Multiple testing; Voronoi tessellations

Indexed keywords

EID: 84903772756     PISSN: 19326157     EISSN: 19417330     Source Type: Journal    
DOI: 10.1214/13-AOAS707     Document Type: Article

References (37)

1. BENJAMINI, Y. and HELLER, R. (2008). Screening for partial conjunction hypotheses. Biometrics 64 1215-1222. MR2522270
2. BENJAMINI, Y. and HOCHBERG, Y. (1995). Controlling the false discovery rate: A practical and powerful approach to multiple testing. J. R. Stat. Soc. Ser. B Stat. Methodol. 57 289-300. MR1325392
3. BENJAMINI, Y. and HOCHBERG, Y. (2000). On the adaptive control of the false discovery rate in multiple testing with independent statistics. J. Educ. Behav. Statist. 25 60-83.
4. BENJAMINI, Y., KRIEGER, A. M. and YEKUTIELI, D. (2006). Adaptive linear step-up procedures that control the false discovery rate. Biometrika 93 491-507. MR2261438
5. DE LICHTENBERG, U., JENSEN, L. J., FAUSBØLL, A., JENSEN, T. S., BORK, P. and BRUNAK, S. (2005). Comparison of computational methods for the identification of cell cycle-regulated genes. Bioinformatics 21 1164-1171.
6. EFRON, B. (2004). Large-scale simultaneous hypothesis testing: The choice of a null hypothesis. J. Amer. Statist. Assoc. 99 96-104. MR2054289
7. EFRON, B. (2007). Correlation and large-scale simultaneous significance testing. J. Amer. Statist. Assoc. 102 93-103. MR2293302
8. FISHER, S. R. A. (1932). Statistical Methods for Research Workers, 4th ed. Oliver & Boyd, Edinburgh.
9. FORBES, S. A., BINDAL, N., BAMFORD, S., COLE, C., KOK, C. Y., BEARE, D., JIA, M., SHEPHERD, R., LEUNG, K., MENZIES, A. et al. (2011). COSMIC: Mining complete cancer genomes in the catalogue of somatic mutations in cancer. Nucleic Acids Res. 39 D945-D950.
10. FRITZ, B., SCHUBERT, F., WROBEL, G., SCHWAENEN, C., WESSENDORF, S., NESSLING, M., KORZ, C., RIEKER, R. J., MONTGOMERY, K., KUCHERLAPATI, R. et al. (2002). Microarraybased copy number and expression profiling in dedifferentiated and pleomorphic liposarcoma. Cancer Res. 62 2993-2998.
11. GHOSH, D. (2011). Generalized Benjamini-Hochberg procedures using spacings. J. Indian Soc. Agricultural Statist. 65 213-220, 262. MR2868128
12. GHOSH, D. (2012). Incorporating the empirical null hypothesis into the Benjamini-Hochberg procedure. Stat. Appl. Genet. Mol. Biol. 11 Art. 11, front matter+19. MR2958610
13. HUANG, D. W., SHERMAN, B. T. and LEMPICKI, R. A. (2008). Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nature Protoc. 4 44-57.
14. HUANG, D. W., SHERMAN, B. T. and LEMPICKI, R. A. (2009). Bioinformatics enrichment tools: Paths toward the comprehensive functional analysis of large gene lists. Nucleic Acids Res. 37 1-13.
15. JIMÉNEZ, R. and YUKICH, J. E. (2002). Asymptotics for statistical distances based on Voronoi tessellations. J. Theoret. Probab. 15 503-541. MR1898817
16. JIN, J. and CAI, T. T. (2007). Estimating the null and the proportional of nonnull effects in largescale multiple comparisons. J. Amer. Statist. Assoc. 102 495-506. MR2325113
17. KIM, J. H., DHANASEKARAN, S. M., MEHRA, R., TOMLINS, S. A., GU, W., YU, J., KUMARSINHA, C., CAO, X., DASH, A., WANG, L. et al. (2007). Integrative analysis of genomic aberrations associated with prostate cancer progression. Cancer Res. 67 8229-8239.
18. LOUGHIN, T. M. (2004). A systematic comparison of methods for combining p-values from independent tests. Comput. Statist. Data Anal. 47 467-485. MR2086483
19. MURALIDHARAN, O. (2010). An empirical Bayes mixture method for effect size and false discovery rate estimation. Ann. Appl. Stat. 4 422-438. MR2758178
20. OKABE, A., BOOTS, B., SUGIHARA, K. and CHIU, S. N. (2010). Spatial Tessellations: Concepts and Applications of Voronoi Diagrams, 2nd ed. Wiley, Chichester.
21. OLIVA, A., ROSEBROCK, A., FERREZUELO, F., PYNE, S., CHEN, H., SKIENA, S., FUTCHER, B. and LEATHERWOOD, J. (2005). The cell cycle-regulated genes of Schizosaccharomyces pombe. PLoS Biol. 3 e225.
22. OWEN, A. B. (2009). Karl Pearson's meta-analysis revisited. Ann. Statist. 37 3867-3892.
23. PHILLIPS, D. and GHOSH, D. (2014a). Supplement to "Testing the disjunction hypothesis using Voronoi diagrams with applications to genetics. " DOI:10.1214/13-AOAS707SUPPA.
24. PHILLIPS, D. and GHOSH, D. (2014b). Supplement to "Testing the disjunction hypothesis using Voronoi diagrams with applications to genetics. " DOI:10.1214/13-AOAS707SUPPB.
25. POLLACK, J. R., SØRLIE, T., PEROU, C. M., REES, C. A., JEFFREY, S. S., LONNING, P. E., TIBSHIRANI, R., BOTSTEIN, D., BØRRESEN-DALE, A.-L. and BROWN, P. O. (2002). Microarray analysis reveals a major direct role of DNA copy number alteration in the transcriptional program of human breast tumors. Proc. Natl. Acad. Sci. USA 99 12963-12968.
26. POUNDS, S. B. (2006). Estimation and control of multiple testing error rates for microarray studies. Brief. Bioinf. 7 25-36.
27. POUNDS, S. and MORRIS, S. W. (2003). Estimating the occurrence of false positives and false negatives in microarray studies by approximating and partitioning the empirical distribution of p-values. Bioinformatics 19 1236-1242.
28. PYKE, R. (1965). Spacings. J. R. Stat. Soc. Ser. B Stat. Methodol. 27 395-449.
29. STOREY, J. D. (2002). A direct approach to false discovery rates. J. R. Stat. Soc. Ser. B Stat. Methodol. 64 479-498. MR1924302
30. STOUFFER, S. A., SUCHMAN, E. A., DEVINNEY, L. C., STAR, S. A. andWILLIAMS JR., R. M. (1949). The American Soldier: Adjustment During Army Life. Stud. Soc. Psychol. World War II 1. Princeton Univ. Press, Princeton.
31. STRIMMER, K. (2008). A unified approach to false discovery rate estimation. BMC Bioinformatics 9 303.
32. TAGNON, H. J., WHITMORE, W. F. and SHULMAN, N. R. (1952). Fibrinolysis in metastatic cancer of the prostate. Cancer 5 9-12.
33. TONON, G., WONG, K.-K., MAULIK, G., BRENNAN, C., FENG, B., ZHANG, Y., KHATRY, D. B., PROTOPOPOV, A., YOU, M. J., AGUIRRE, A. J. et al. (2005). High-resolution genomic profiles of human lung cancer. Proc. Natl. Acad. Sci. USA 102 9625-9630.
34. TSAFRIR, D., BACOLOD, M., SELVANAYAGAM, Z., TSAFRIR, I., SHIA, J., ZENG, Z., LIU, H., KRIER, C., STENGEL, R. F., BARANY, F. et al. (2006). Relationship of gene expression and chromosomal abnormalities in colorectal cancer. Cancer Res. 66 2129-2137.
35. TURNER, R. (2013). deldir: Delaunay triangulation and Dirichlet (Voronoi) tessellation.
36. WILKINSON, B. (1951). A statistical consideration in psychological research. Psychol. Bull. 48 156.
37. ZACHARSKI, L. R., WOJTUKIEWICZ, M. Z., COSTANTINI, V., ORNSTEIN, D. L., MEMOLI, V. A. et al. (1992). Pathways of coagulation/fibrinolysis activation in malignancy. Semin. Thromb. Hemost. 18 104.