A fast Bayesian change point analysis for the segmentation of microarray data

Bioinformatics

Volumn 24, Issue 19, 2008, Pages 2143-2148

  Erdman, Chandra ^a   Emerson, John W ^a  

^a YALE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ACCURACY; ALGORITHM; ARTICLE; ARTIFICIAL CHROMOSOME; BAYES THEOREM; BIOINFORMATICS; CHROMOSOME ABERRATION; GENE MUTATION; GENE SEQUENCE; GENOME ANALYSIS; GLIOBLASTOMA; HUMAN; MATHEMATICAL COMPUTING; MICROARRAY ANALYSIS; PRIORITY JOURNAL; SEQUENCE ANALYSIS; SIGNAL NOISE RATIO; SIMULATION;

EID: 52949087226     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/btn404     Document Type: Article

References (31)

1. Bai,J. and Perron,P. (2003) Computation and analysis of multiple structural change models. J. Appl. Econom., 18, 1-22.
2. Barry,D. and Hartigan,J.A. (1993) A Bayesian analysis for change point problems. J. Am. Stat. Assoc., 88, 309-319.
3. Bredel,M. et al. (2005) High-resolution genome-wide mapping of genetic alterations in human glial brain tumors. Cancer Res., 65, 4088-4096.
4. Cleveland,W.S. (1979) Robust locally weighted regression smoothing scatterplots. J. Am. Stat. Assoc., 74, 829-836.
5. Eiters,P.H.C. and Menezes,R.X. (2004) Quantile smoothing of array CGH data. Bioinformatics, 21, 1146-1153.
6. Erdman,C. and Emerson,J.W. (2007) bcp: An R package for performing a Bayesian analysis of change point problems. J. Stat. Software, 23, 1-13.
7. Erdman,C. and Emerson,J.W. (2008) bcp: An R Package for Performing a Bayesian Analysis of Change Point Problems. R package version 1-2. Available at http://cran.r-project.org/ (last accessed date June 16, 2008).
8. Fridlyand,J. et al. (2004) Hidden Markov models approach to the analysis of array CGH data. J. Multivar. Anal., 90, 132-153.
9. Garcia,R. and Perron,P. (1996) An analysis of the real interest rate under regime shifts. Rev. Econom. Stat., 78, 111-125.
10. Hsu,L. et al. (2005) Denoising array-based comparative genomic hybridization data using wavelets. Biostatistics, 6, 211-226.
11. Hupe,P. et al. (2004) Analysis of array CGH data: From signal ratio to gain and loss of DNA regions. Bioinformalics, 20, 3413-3422.
12. Jong,K. et al. (2003) Chromosomal breakpoint detection in human cancer. Lect. Notes Comput. Sci., 2611, 54-65.
13. Kallioniemi,A. et al. (1992) Comparative genomic hybridization for molecular cytogenetic analysis of solid tumors. Science, 258 818-421.
14. Lai,W.R. et al. (2005) Comparative analysis of algorithms for identifying amplifications and deletions in array CGH data. Bioinformatics, 21, 3763-3770.
15. Lingjaerde,O.C. et al. (2005) CGH-Explorer. a program for analysis of array-CGH data. Bioinformatics, 21, 821-822.
16. Myers,C. et al. (2004) Accurate detection of aneuploidies in array CGH and gene expression microarray data. Bioinformatics, 20, 3533-3543.
17. Picard,F. et al. (2005) A statistical approach for array CGH data analysis. BMC Bioinformatics, 6, 1471-2105.
18. Olshen,A.B. and Venketraman,E.S. (2004) Circular binary segmentation for the analysis of array-based DNA copy number data. Biostatistics, 5, 557-572.
19. Plummer,M. et al. (2007) coda: Output Analysis and Diagnostics for MCMC. R package version 0.12-1. Available at http://cran.r-projectorg/ (last accessed date June 16, 2008).
20. Polzehl,J. and Spokiony,V. (2000) Adaptive weights smoothing with applications to image restoration. J. R. Stat. Soc. B, 62, 335-354.
21. R Development Core Team (2008) R: A language and environment for statistical computing. Available at http://www.R-project.org.
22. REvolution Computing with support and contributions from Pfizer (2008) nws: R functions for NetWorkSpaces and Sleigh. R package version 1.6.3. Available at http://nws-r.sourceforge.net. (last accessed date June 16, 2008).
23. Sen,A. and Srivastava,M. (1975) On tests for detecting change in mean. Ann. Stat., 3, 98-108.
24. Snijders,A. et al. (2001) Assembly of microarrays for genome-wide measurement of DNA copy number. Nat. Genet., 29, 263-246.
25. Venkatraman,E.S. and Olshen,A.B. (2007a) DNAcopy: A Package for Analyzing DNA Copy Data. R package version 1.6.0. Available at http://www.bioconductor.org/packages/2.2/bioc.html/DNAcopy.html (last accessed date June 16, 2008).
26. Venkatraman,E.S. and Olshen,A.B. (2007b) A faster circular binary segmentation for the analysis of array CGH data. Bioinformatics, 23, 657-683.
27. Wang,P. et al. (2005) A method for calling gains and losses in array CGH data. Biostatistics, 6, 45-58.
28. Yao,Y.C. (1984) Estimation of a noisy discrete-time step function: Bayes and empirical Bayes approaches. Ann. Stat., 12, 1434-1447.
29. Zoileis,A. et al. (2002) strucchange: An R package for testing for structural change in linear regression models. J. Stat. Software, 7, 1-38.
30. Zeileis,A. et al. (2003) Testing and dating of structural changes in practice. Comput. Stat. Data Anal., 44, 109-123.
31. Zeileis,A. et al. (2007) strucchange: Testing, Monitoring and Dating Structural Changes. R package version 1.3-2. Available at http://cran.r-project.org/ (last accessed date June 16, 2008).