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Volumn 5, Issue 2 B, 2011, Pages 1360-1378

False discovery rates in somatic mutation studies of cancer

Author keywords

Cancer genome studies; False discovery rate; Genome wide studies; Multiple hypothesis testing; Somatic mutations

Indexed keywords


EID: 84862797765     PISSN: 19326157     EISSN: 19417330     Source Type: Journal    
DOI: 10.1214/10-AOAS438     Document Type: Article
Times cited : (9)

References (35)
  • 1
    • 0001677717 scopus 로고
    • Controlling the false discovery rate: A practical and powerful approach to multiple testing
    • Mathematical Reviews (MathSciNet): MR1325392
    • 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. Mathematical Reviews (MathSciNet): MR1325392
    • (1995) J. Roy. Statist. Soc. Ser. B , vol.57 , pp. 289-300
    • Benjamini, Y.1    Hochberg, Y.2
  • 2
    • 0035733108 scopus 로고    scopus 로고
    • The control of the false discovery rate in multiple testing under dependency
    • Mathematical Reviews (MathSciNet): MR1869245 Zentralblatt MATH: 1041.62061 Digital Object Identifier: doi:10.1214/aos/1013699998 Project Euclid: euclid.aos/1013699998
    • Benjamini, Y. and Yekutieli, D. (2001). The control of the false discovery rate in multiple testing under dependency. Ann. Statist. 29 1165-1188. Mathematical Reviews (MathSciNet): MR1869245 Zentralblatt MATH: 1041.62061 Digital Object Identifier: doi:10.1214/aos/1013699998 Project Euclid: euclid.aos/1013699998
    • (2001) Ann. Statist , vol.29 , pp. 1165-1188
    • Benjamini, Y.1    Yekutieli, D.2
  • 3
    • 0002617436 scopus 로고
    • Ferguson distributions via Pólya urn schemes
    • Mathematical Reviews (MathSciNet): MR362614 Digital Object Identifier: doi:10.1214/aos/1176342372 Project Euclid: euclid.aos/1176342372
    • Blackwell, D. and MacQueen, J. B. (1973). Ferguson distributions via Pólya urn schemes. Ann. Statist. 1 353-355. Mathematical Reviews (MathSciNet): MR362614 Digital Object Identifier: doi:10.1214/aos/1176342372 Project Euclid: euclid.aos/1176342372
    • (1973) Ann. Statist , vol.1 , pp. 353-355
    • Blackwell, D.1    Macqueen, J.B.2
  • 4
    • 54549108740 scopus 로고    scopus 로고
    • Comprehensive genomic characterization defines human glioblastoma genes and core pathways
    • The Cancer Genome Atlas project
    • The Cancer Genome Atlas project. (2008). Comprehensive genomic characterization defines human glioblastoma genes and core pathways. Nature 455 1061-1068.
    • (2008) Nature , vol.455 , pp. 1061-1068
  • 5
    • 54949139489 scopus 로고    scopus 로고
    • False discovery rate paradigms for statistical analyses of microarray gene expression data
    • Cheng, C. and Pounds, S. (2007). False discovery rate paradigms for statistical analyses of microarray gene expression data. Bioinformation 1 436-446.
    • (2007) Bioinformation , vol.1 , pp. 436-446
    • Cheng, C.1    Pounds, S.2
  • 6
    • 54549110274 scopus 로고    scopus 로고
    • Resampling-based empirical Bayes multiple testing procedures for controlling generalized tail probability and expected value error rates: Focus on the false discovery rate and simulation study
    • Mathematical Reviews (MathSciNet): MR2542339 Digital Object Identifier: doi:10.1002/bimj.200710473
    • Dudoit, S., Gilbert, H. and Laan, M. V. D. (2008). Resampling-based empirical Bayes multiple testing procedures for controlling generalized tail probability and expected value error rates: Focus on the false discovery rate and simulation study. Biom. J. 50 716-744. Mathematical Reviews (MathSciNet): MR2542339 Digital Object Identifier: doi:10.1002/bimj.200710473
    • (2008) Biom. J , vol.50 , pp. 716-744
    • Dudoit, S.1    Gilbert, H.2    Laan, M.V.D.3
  • 7
    • 0043203327 scopus 로고    scopus 로고
    • Multiple hypothesis testing in microarray experiments
    • Mathematical Reviews (MathSciNet): MR1997066 Digital Object Identifier: doi:10.1214/ss/1056397487 Project Euclid: euclid.ss/1056397487
    • Dudoit, S., Shaffer, J. P. and Boldrick, J. C. (2003). Multiple hypothesis testing in microarray experiments. Statist. Sci. 18 71-103. Mathematical Reviews (MathSciNet): MR1997066 Digital Object Identifier: doi:10.1214/ss/1056397487 Project Euclid: euclid.ss/1056397487
    • (2003) Statist. Sci , vol.18 , pp. 71-103
    • Dudoit, S.1    Shaffer, J.P.2    Boldrick, J.C.3
  • 8
    • 70350094855 scopus 로고    scopus 로고
    • Nonparametric Bayes applications to biostatistics
    • Cambridge Univ. Press, Cambridge, Mathematical Reviews (MathSciNet): MR2730665 Digital Object Identifier: doi:10.1017/CBO9780511802478.008
    • Dunson, D. B. (2010). Nonparametric Bayes applications to biostatistics. In Bayesian Nonparametrics. Camb. Ser. Stat. Probab. Math. 223-273. Cambridge Univ. Press, Cambridge. Mathematical Reviews (MathSciNet): MR2730665 Digital Object Identifier: doi:10.1017/CBO9780511802478.008
    • (2010) Bayesian Nonparametrics. Camb. Ser. Stat. Probab. Math , pp. 223-273
    • Dunson, D.B.1
  • 9
    • 0038364283 scopus 로고    scopus 로고
    • Robbins, empirical Bayes and microarrays
    • Mathematical Reviews (MathSciNet): MR1983533 Zentralblatt MATH: 1038.62099 Digital Object Identifier: doi:10.1214/aos/1051027871 Project Euclid: euclid.aos/1051027871
    • Efron, B. (2003). Robbins, empirical Bayes and microarrays. Ann. Statist. 31 366-378. Mathematical Reviews (MathSciNet): MR1983533 Zentralblatt MATH: 1038.62099 Digital Object Identifier: doi:10.1214/aos/1051027871 Project Euclid: euclid.aos/1051027871
    • (2003) Ann. Statist , vol.31 , pp. 366-378
    • Efron, B.1
  • 10
    • 1542784653 scopus 로고    scopus 로고
    • Empirical Bayes analysis of a microarray experiment
    • Mathematical Reviews (MathSciNet): MR1946571 Zentralblatt MATH: 1073.62511 Digital Object Identifier: doi:10.1198/016214501753382129
    • Efron, B., Tibshirani, R., Storey, J. D. and Tusher, V. (2001). Empirical Bayes analysis of a microarray experiment. J. Amer. Statist. Assoc. 96 1151-1160. Mathematical Reviews (MathSciNet): MR1946571 Zentralblatt MATH: 1073.62511 Digital Object Identifier: doi:10.1198/016214501753382129
    • (2001) J. Amer. Statist. Assoc , vol.96 , pp. 1151-1160
    • Efron, B.1    Tibshirani, R.2    Storey, J.D.3    Tusher, V.4
  • 11
    • 84950937290 scopus 로고
    • Bayesian density estimation and inference using mixtures
    • Mathematical Reviews (MathSciNet): MR1340510 Zentralblatt MATH: 0826.62021 Digital Object Identifier: doi:10.1080/01621459.1995.10476550
    • Escobar, M. D. and West, M. (1995). Bayesian density estimation and inference using mixtures. J. Amer. Statist. Assoc. 90 577-588. Mathematical Reviews (MathSciNet): MR1340510 Zentralblatt MATH: 0826.62021 Digital Object Identifier: doi:10.1080/01621459.1995.10476550
    • (1995) J. Amer. Statist. Assoc , vol.90 , pp. 577-588
    • Escobar, M.D.1    West, M.2
  • 12
    • 55249117952 scopus 로고    scopus 로고
    • A review of modern multiple hypothesis testing, with particular attention to the false discovery proportion
    • Mathematical Reviews (MathSciNet): MR2526659 Zentralblatt MATH: 1156.62048 Digital Object Identifier: doi:10.1177/0962280206079046
    • Farcomeni, A. (2008). A review of modern multiple hypothesis testing, with particular attention to the false discovery proportion. Stat. Methods Med. Res. 17 347-388. Mathematical Reviews (MathSciNet): MR2526659 Zentralblatt MATH: 1156.62048 Digital Object Identifier: doi:10.1177/0962280206079046
    • (2008) Stat. Methods Med. Res , vol.17 , pp. 347-388
    • Farcomeni, A.1
  • 13
    • 0001120413 scopus 로고
    • A Bayesian analysis of some nonparametric problems
    • Mathematical Reviews (MathSciNet): MR350949 Zentralblatt MATH: 0255.62037 Digital Object Identifier: doi:10.1214/aos/1176342360 Project Euclid: euclid.aos/1176342360
    • Ferguson, T. S. (1973). A Bayesian analysis of some nonparametric problems. Ann. Statist. 1 209-230. Mathematical Reviews (MathSciNet): MR350949 Zentralblatt MATH: 0255.62037 Digital Object Identifier: doi:10.1214/aos/1176342360 Project Euclid: euclid.aos/1176342360
    • (1973) Ann. Statist , vol.1 , pp. 209-230
    • Ferguson, T.S.1
  • 14
    • 34548679336 scopus 로고    scopus 로고
    • The consensus coding sequences of human breast and colorectal cancers
    • Comment on, (author reply 1500)
    • Forrest, W. F. and Cavet, G. (2007). Comment on "The consensus coding sequences of human breast and colorectal cancers." Science 317 1500 (author reply 1500).
    • (2007) Science , vol.317 , pp. 1500
    • Forrest, W.F.1    Cavet, G.2
  • 16
    • 33747869580 scopus 로고    scopus 로고
    • Statistical analysis of pathogenicity of somatic mutations in cancer
    • Greenman, C., Wooster, R., Futreal, P. A., Stratton, M. R. and Easton, D. F. (2006). Statistical analysis of pathogenicity of somatic mutations in cancer. Genetics 173 2187-2198.
    • (2006) Genetics , vol.173 , pp. 2187-2198
    • Greenman, C.1    Wooster, R.2    Futreal, P.A.3    Stratton, M.R.4    Easton, D.F.5
  • 18
    • 33646253378 scopus 로고    scopus 로고
    • Efficient two-stage genome-wide association designs based on false positive report probabilities
    • Kraft, P. (2006). Efficient two-stage genome-wide association designs based on false positive report probabilities. Pac. Symp. Biocomput. 523-534.
    • (2006) Pac. Symp. Biocomput , pp. 523-534
    • Kraft, P.1
  • 19
    • 4043092820 scopus 로고    scopus 로고
    • Nonparametric Bayesian data analysis
    • Mathematical Reviews (MathSciNet): MR2082149 Digital Object Identifier: doi:10.1214/088342304000000017 Project Euclid: euclid.ss/1089808275
    • Müller, P. and Quintana, F. A. (2004). Nonparametric Bayesian data analysis. Statist. Sci. 19 95-110. Mathematical Reviews (MathSciNet): MR2082149 Digital Object Identifier: doi:10.1214/088342304000000017 Project Euclid: euclid.ss/1089808275
    • (2004) Statist. Sci , vol.19 , pp. 95-110
    • Müller, P.1    Quintana, F.A.2
  • 22
    • 57049128193 scopus 로고    scopus 로고
    • Design and analysis issues in genome-wide somatic mutation studies of cancer
    • Parmigiani, G., Boca, S., Lin, J., Kinzler, K. and Velculescu, V. (2009). Design and analysis issues in genome-wide somatic mutation studies of cancer. Genomics 93 17-21.
    • (2009) Genomics , vol.93 , pp. 17-21
    • Parmigiani, G.1    Boca, S.2    Lin, J.3    Kinzler, K.4    Velculescu, V.5
  • 24
    • 34548679336 scopus 로고    scopus 로고
    • Comment on "The consensus coding sequences of human breast and colorectal cancers
    • Rubin, A. F. and Green, P. (2007). Comment on "The consensus coding sequences of human breast and colorectal cancers." Science 317 1500.
    • (2007) Science , vol.317 , pp. 1500
    • Rubin, A.F.1    Green, P.2
  • 25
    • 0042859846 scopus 로고    scopus 로고
    • Optimal two-stage genotyping in population-based association studies
    • Satagopan, J. M. and Elston, R. C. (2003). Optimal two-stage genotyping in population-based association studies. Genet. Epidemiol. 25 149-157.
    • (2003) Genet. Epidemiol , vol.25 , pp. 149-157
    • Satagopan, J.M.1    Elston, R.C.2
  • 26
    • 4444317393 scopus 로고    scopus 로고
    • Two-stage designs for gene-desease association studies with sample size constraints
    • Mathematical Reviews (MathSciNet): MR2089433 Digital Object Identifier: doi:10.1111/j.0006-341X.2004.00207.x
    • Satagopan, J. M., Venkatraman, E. S. and Begg, C. B. (2004). Two-stage designs for gene-desease association studies with sample size constraints. Biometrics 60 589-597. Mathematical Reviews (MathSciNet): MR2089433 Digital Object Identifier: doi:10.1111/j.0006-341X.2004.00207.x
    • (2004) Biometrics , vol.60 , pp. 589-597
    • Satagopan, J.M.1    Venkatraman, E.S.2    Begg, C.B.3
  • 27
    • 0036188784 scopus 로고    scopus 로고
    • Two-stage designs for gene-disease association studies
    • Mathematical Reviews (MathSciNet): MR1891375, Digital Object Identifier: doi:10.1111/j.0006-341X.2002.00163.x
    • 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. Mathematical Reviews (MathSciNet): MR1891375 Digital Object Identifier: doi:10.1111/j.0006-341X.2002.00163.x
    • (2002) Biometrics , vol.58 , pp. 163-170
    • Satagopan, J.M.1    Verbel, D.A.2    Venkatraman, E.S.3    Offit, K.E.4    Begg, C.B.5
  • 29
    • 31744435871 scopus 로고    scopus 로고
    • Joint analysis is more efficient than replication-based analysis for two-stage genome-wide association studies
    • Skol, A. D., Scott, L. J., Abecasis, G. R. and Boehnke, M. (2006). Joint analysis is more efficient than replication-based analysis for two-stage genome-wide association studies. Nat. Genet. 38 209-213.
    • (2006) Nat. Genet , vol.38 , pp. 209-213
    • Skol, A.D.1    Scott, L.J.2    Abecasis, G.R.3    Boehnke, M.4
  • 30
    • 37349019755 scopus 로고    scopus 로고
    • Boa: An R package for MCMC output convergence assessment and posterior inference
    • Smith, B. (2007). boa: An R package for MCMC output convergence assessment and posterior inference. Journal of Statistical Software 21 1-37.
    • Journal of Statistical Software , vol.21 , pp. 1-37
    • Smith, B.1
  • 31
    • 0036020892 scopus 로고    scopus 로고
    • A direct approach to false discovery rates
    • Mathematical Reviews (MathSciNet): MR1924302 Zentralblatt MATH: 1090.62073 Digital Object Identifier: doi:10.1111/1467-9868.00346
    • Storey, J. D. (2002). A direct approach to false discovery rates. J. R. Stat. Soc. Ser. B Stat. Methodol. 64 479-498. Mathematical Reviews (MathSciNet): MR1924302 Zentralblatt MATH: 1090.62073 Digital Object Identifier: doi:10.1111/1467-9868.00346
    • (2002) J. R. Stat. Soc. Ser. B Stat. Methodol , vol.64 , pp. 479-498
    • Storey, J.D.1
  • 33
    • 79952195487 scopus 로고    scopus 로고
    • Gamma shape mixtures for heavy-tailed distributions
    • Mathematical Reviews (MathSciNet): MR2524355 Zentralblatt MATH: 05591297 Digital Object Identifier: doi:10.1214/07-AOAS156 Project Euclid: euclid.aoas/1215118537
    • Venturini, S., Dominici, F. and Parmigiani, G. (2008). Gamma shape mixtures for heavy-tailed distributions. Ann. Appl. Statist. 2 756-776. Mathematical Reviews (MathSciNet): MR2524355 Zentralblatt MATH: 05591297 Digital Object Identifier: doi:10.1214/07-AOAS156 Project Euclid: euclid.aoas/1215118537
    • (2008) Ann. Appl. Statist , vol.2 , pp. 756-776
    • Venturini, S.1    Dominici, F.2    Parmigiani, G.3
  • 34
    • 33750356125 scopus 로고    scopus 로고
    • Optimal two-stage genome-wide association designs based on false discovery rate
    • Mathematical Reviews (MathSciNet): MR2297463
    • Wang, H. and Stram, D. O. (2006). Optimal two-stage genome-wide association designs based on false discovery rate. Comput. Statist. Data Anal. 51 457-465. Mathematical Reviews (MathSciNet): MR2297463
    • (2006) Comput. Statist. Data Anal , vol.51 , pp. 457-465
    • Wang, H.1    Stram, D.O.2


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