Spike and slab gene selection for multigroup microarray data

Journal of the American Statistical Association

Volumn 100, Issue 471, 2005, Pages 764-780

  Ishwaran, Hemant ^a   Rao, J Sunil ^b  

^a LERNER RESEARCH INSTITUTE   (United States)

^b CASE WESTERN RESERVE UNIVERSITY   (United States)

Author keywords

Colon cancer; Hypervariance; Penalization; Rescaling; Risk misclassification; Shrinkage; Sparsity; Stochastic variable selection; Zcut

Indexed keywords

EID: 22944431540     PISSN: 01621459     EISSN: None     Source Type: Journal    
DOI: 10.1198/016214505000000051     Document Type: Review

References (18)

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, Ser. B, 57, 289-300.
2. Cohen, A., Minsky, B., and Schilsky, R. (1997), "Cancer of the Colon," in Cancer: Principles and Practice of Oncology (5th ed.), eds. V. T. J. De Vita, S. Hellman, and S. Rosenberg, Philadelphia, PA: Lippincott-Raven Publishers, pp. 1144-1196.
3. Dang, C. V., and Semenza, G. L. (1999), "Oncogenic Alterations of Metabolism," Trends in Biochemical Science, 24, 68-72.
4. Durbin, B., Hardin, J., Hawkins, D., and Rocke, D. M. (2002), "A Variance-Stabilizing Transformation for Gene-Expression Microarray Data," Bioinformatics, 18, S105-S110.
5. Efron, B., Tibshirani, R., Storey, J. D., and Tusher, V. G. (2001), "Empirical Bayes Analysis of a Microarray Experiment," Journal of the American Statical Association, 96, 1151-1160.
6. Genovese, C., and Wasserman, L. (2002), "Operating Characteristics and Extensions of the FDR Procedure," Journal of the Royal Statistical Society, Ser. B, 64, 499-517.
7. George, E. I., and McCulloch, R. E. (1993), "Variable Selection via Gibbs Sampling," Journal of the American Statistical Association, 88, 881-889.
8. Hegde, P., Qi, R., Gaspard, R., Abernathy, K., Dharap, S., Earle-Hughes, J., Gay, C., Nwokekeh, N. U., Chen, T., Saeed, A. I., Sharov, V., Lee, N. H., Yeatman, T. J., and Quackenbush, J. (2001), "Identification of Tumor Markers in Models of Human Colorectal Cancer Using a 19,200-Element Complementary DNA Microarray," Cancer Research, 61, 7192-7191.
9. Ishwaran, H., and Rao, J. S. (2003), "Detecting Differentially Expressed Genes in Microarrays Using Bayesian Model Selection," Journal of the American Statistical Association, 98, 438-455.
10. _ (2005), "Spike and Slab Variable Selection: Frequentist and Bayesian Strategies," The Annals of Statistics, 33, 730-773.
11. John, A. P. (2001), "Dysfunctional Mitochondria, Not Oxygen Insufficiency, Cause Cancer Cells to Produce Inordinate Amounts of Lactic Acid: The Impact of This on the Treatment of Cancer," Medical Hypotheses, 57, 429-431.
12. Kendziorski, C. M., Newton, M. A., Lan, H., and Gould, M. N. (2003), "On Parametric Empirical Bayes Methods for Comparing Multiple Groups Using Replicated Gene Expression Profiles," Statistics in Medicine, 22, 3899-3914.
13. Liu, G., Loraine, A. E., Shigeta, R., Cline, M., Cheng, J., Valmeekam, V., Sun, S., Kulp, D., and Siani-Rose, M. A. (2003), "NetAffix: Affymetrix Probesets and Annotations," Nucleic Acids Research, 31, 82-86.
14. Nelson, N. J. (1998), "Quest for New and Better Colon Cancer Treatments Picks Up Steam," Journal of the National Cancer Institute, 90, 1858-1859.
15. Nguyen, D., Arpat, A. B., Wang, N., and Carroll, R. J. (2002), "DNA Microarray Experiments: Biological and Technological Aspects," Biometrics, 58, 701-717.
16. Quillin, P. (2000), "Cancer's Sweet Tooth," Nutrition Science News, 4, 1-8.
17. Storey, J. D. (2002), "A Direct Approach to False Discovery Rates," Journal of the Royal Statistical Society, Ser. B, 64, 479-498.
18. Tusher, V. G., Tibshirani, R., and Chu, G. (2001), "Significance Analysis of Microarrays Applied to the Ionizing Radiation Response," Proceedings of the National Academy of Science, 98, 5116-5121.