Bayesian analysis of comparative microarray experiments by model averaging

Bayesian Analysis

Volumn 1, Issue 4, 2006, Pages 707-732

  Sebastiani, Paola ^a   Xiey, Hui ^a   Ramoni, Marco F ^b  

^a BOSTON UNIVERSITY   (United States)

^b BOSTON CHILDREN S HOSPITAL   (United States)

Author keywords

False discovery rate; Gamma distribution; Gene expression; Log normal distribution; Microarrays; Model averaging; True and false positive rates

Indexed keywords

EID: 46049099698     PISSN: 19360975     EISSN: 19316690     Source Type: Journal    
DOI: 10.1214/06-BA123     Document Type: Article

References (28)

1. Baldi, P. and Long, A. D. (2001). "A Bayesian Framework for the Analysis of Microarray Expression Data: Regularized T-Test and Statistical Inferences of Gene Changes." Bioinformatics, 17: 509-519
2. Chen, Y., Dougherty, E., and Bittner, M. (1997). "Ratio-based Decisions and the Quantitative Analysis of cDNA Microarray Images." Journal of Biomedical Optics, 2: 364-374
3. Cope, L. M., Irizarry, R. A., Jaffee, H. A., Wu, Z., and Speed, T. P. (2004). "A Benchmark for Affymetrix GeneChip Expression Measures." Bioinformatics, 20: 323-331
4. Dudoit, S., Yang, Y. H., Callow, M. J., and Speed, T. P. (2001). "Statistical Methods for Identifying Genes with Differential Expression in Replicated cDNA Microarrays Experiments." Statistica Sinica, 12: 111-139.
5. Duggan, J. D., Bittner, M., Chen, Y., Meltzer, P., and Trent, J. M. (1999). "Expression Proling Using CDNA Microarrays." Nature Genetics, 21: 10-14.
6. Efron, B., Storey, J. D., and Tibshirani, R. (2001). "Empirical Bayes Analysis of a Microarray Experiment." Journal of the American Statistical Association, 96: 1151-1160
7. Gelman, A. (1996). "Inference and monitoring convergence." In Gilks, W. R., Richard-son, S., and Spiegelhalter, D. J. (eds.), Markov Chain Monto Carlo in Practice, 131-143. Boca Raton, FL: Chapman and HallCRC
8. Gentleman, R. and Carey, V. (2002). "Bioconductor." R News, 2(1): 11-16. URL http://CRAN.R-project.org/doc/Rnews/
9. Giles, P. J. and Kipling, D. (2003). "Normality of Oligonucleotide Microarray Data and Implications for Parametric Statistical Analyses." Bioinformatics, 19: 2254-2262.
10. Hoeting, J. A., Madigan, D., Raftery, A. E., and Volinsky, C. T. (1999). "Bayesian Model Averaging: A Tutorial (with discussion)." Statistical Science, 14: 382-417.
11. Ibrahim, J. G., Chen, M. H., and Gray, R. J. (2002). "Bayesian Models for Gene Expres-sion With DNA Microarray Data." Journal of the American Statistical Association, 97: 88-99.
12. Jacob, F. and Monod, J. (1961). "Genetic Regulatory Mechanisms in the Synthesis of Proteins." Journal of Molecular Biology, 3: 318-356
13. Li, C. and Wong, W. H. (2001). "Model-Based Analysis of Oligonucleotide Arrays: Expression Index Computation and Outlier Detection." Proceedings of the National Academy of Science, USA, 98: 31-36.
14. Lockhart, D., Dong, H., Byrne, M., Follettie, M., Gallo, M., Chee, M., Mittmann, M., Wang, C., Kobayashi, M., Horton, H., and Brown, E. (1996). "Expression monitoring by hybridization to high-density oligonucleotide arrays." Nature Biotechnology, 14: 1675-1680.
15. Montano, M., Rarick, M., Sebastiani, P., Brinkmann, P., Russell, M., Essex, A. N. M., Wester, C., and Thior, I. (2006). "Gene-Expression Proling of HIV-1 Infection and Perinatal Transmission in Southern Africa." Genes and Immunity. In press
16. Nadon, R. and Shoemaker, J. (2002). "Statistical Issues with Microarrays: Processing and Analysis." Trends in Genetics, 18: 265-271.
17. Newton, M. A., Kendziorski, C. M., Richmond, C. S., Blattner, F. R., and Tsui, K. W. (2001). "On differential variability of expression ratios: Improving statistical inference about gene expression changes from microarray data." Journal of Computational Biology, 8(1): 37-52.
18. Reich, M., Ohm, K., Tamayo, P., Angelo, M., and Mesirov, J. P. (2004). "GeneCluster 2.0: An Advanced Toolset for Bioarray Analysis." Bioinformatics, 20(11): 1797-8.
19. Sebastiani, P., Gussoni, E., Kohane, I. S., and Ramoni, M. (2003a). Statistical chal-lenges in functional genomics (with discussion). Statistical Science, 18: 33-70.
20. Sebastiani, P., Jeneralczuk, J., and Ramoni, M. (2006). "Design and Analysis of Screen-ing Experiments with Microarrays." In Dean, A. and Lewis, S. (eds.), Screening, 115-138. Springer.
21. Sebastiani, P. and Ramoni, M. (2002). "Bayesian Differential Analysis of Gene Ex-pression Data." In Proceedings of the Joint Statistical Meeting. Section on Bayesian Statistical Science. American Statistical Association.
22. Sebastiani, P., Yu, Y. H., and Ramoni, M. F. (2003b). "Bayesian Machine Learning and Its Potential Applications to the Genomic Study of Oral Oncology." Advances in Dental Research, 17: 104-108.
23. Shoemaker, J. S. and Lin, S. M. (2005). Methods of Microarray Analysis IV. New York NY: Springer
24. The Tumor Analysis Best Practices Working Group (2004). "Expression Proling -Best Practices for Data Generation and Interpretation of Clinical Trials." Nature Genetics, 5: 229-237
25. Thomas, A., Spiegelhalter, D. J., and Gilks, W. R. (1992). "BUGS: A program to perform Bayesian inference using Gibbs Sampling." In Bernardo, J., Berger, J., Dawid, A. P., and Smith, A. F. M. (eds.), Bayesian Statistics 4, 837-42. Oxford, UK: Oxford University Press.
26. Thomas, J. G., Olson, J. M., Tapscott, S. J., and Zhao, L. P. (2001). "An Ecient and Robust Statistical Modeling Approach to Discover Differentially Expressed Genes Using Genomic Expression Proles." Genome Research, 11: 1227-1236.
27. Tusher, V. G., Tibshirani, R., and Chu, G. (2000). "Signicance Analysis of Microarrays Applied to the Ionizing Radiation Response." Proceedings of the National Academy of Science, USA, 98: 5116-5121
28. Zien, A., Fluck, J., Zimmer, R., and Lengauer, T. (2003). Microarrays: How Many Do You Need?" Journal of Computational Biology, 10(3-4): 653-67.