Quality control and robust estimation for cDNA microarrays with replicates

Journal of the American Statistical Association

Volumn 101, Issue 473, 2006, Pages 30-40

  Gottardo, Raphael ^a   Raftery, Adrian E ^b   Yeung, Ka Yee ^b   Bumgarner, Roger E ^b  

^a UNIVERSITY OF BRITISH COLUMBIA   (Canada)

^b UNIVERSITY OF WASHINGTON   (United States)

Author keywords

Bayesian hierarchical model; Gene filtering; Heteroscedasticity; Markov chain Monte Carlo; Outlier; Quality control; T distribution

Indexed keywords

EID: 33645529198     PISSN: 01621459     EISSN: None     Source Type: Journal    
DOI: 10.1198/016214505000001096     Document Type: Article

References (42)

1. Besag, J. E., and Higdon, D. M. (1999), "Bayesian Analysis of Agricultural Field Experiments," Journal of the Royal Statistical Society, Ser. B, 61, 691-746.
2. Box, G. E. P., and Cox, D. R. ( 1964), "An Analysis of Transformations," Journal of the Royal Statistical Society, Ser. B, 26, 211-252.
3. _ (1982), "An Analysis of Transformations Revisited, Rebutted," Journal of the American Statistical Association, 77, 209-210.
4. Brown, C. S., Goodwin, P. C., and Sorger, P. K. (2001), "Image Metrics in the Statistical Analysis of DNA Microarray Data," Proceedings of the National Academy of Science USA, 98, 8944-8949.
5. Celeux, G., Hum, M., and Robert, C. (2000), "Computational and Inferential Difficulties With Mixture Posterior Distributions," Journal of the American Statistical Association, 95, 957-970.
6. Chen, J. J., Delongchamp, R. R., Tsai, C., Hsueh, H., Sistare, F., Thompson, K. L., Desai, V. G., and Fuscoe, J. C. (2003), "Analysis of Variance Components in Gene Expression Data," Bioinformatics, 20, 1436-1446.
7. Chen, Y., Dougherty, E. R., and Bittner, M. L. (1997), "Ratio-Based Decisions and the Quantitative Analysis of cDNA Microarray Images," Journal of Biomedical Optics, 1, 364-374.
8. Churchill, G. A. (2002), "Fundamentals of Experimental Design for cDNA Microarrays," Nature Genetics, 32, 490-495.
9. Cleveland, W. S. (1979), "Robust Locally Weighted Regression and Smoothing Scatterplots," Journal of American Statistical Association, 74, 829-836.
10. Cui, X., Hwang, J. T. G., Qiu, J., Blades, N. J., and Churchill, G. A. (2005), "Improved Statistical Tests for Differential Gene Expression by Skrinking Variance Components Estimates," Biostatistics, 6, 59-75.
11. Cui, X., Kerr, M. K., and Churchill, G. A. (2002), "Data Transformations for cDNA Microarray Data," technical report, The Jackson Laboratory.
12. Dixon, W. J. (1950), "Analysis of Extreme Values," The Annals of Mathematical Statistics, 21, 488-506.
13. Dobbin, K., Shin, J. H., and Simon, R. (2003), "Questions and Answers for Identifying Differentially Expressed Genes," Journal of the National Cancer Institute, 95, 1362-1369.
14. Dudoit, S., Yang, Y. H., Callow, M. J., and Speed, T. P. (2002), "Statistical Methods for Identifying Differentially Expressed Genes in Replicated cDNA Microarray Experiments," Statistica Sinica, 12, 111-139.
15. Durbin, B., Hardin, J., Hawkins, D., and Rocke, D. M. (2002), "A Variance-Stabilizing Transformation for the Gene-Expression Microarray Data," Bioinformatics, 18, 105S-110S.
16. Gelfand, A. E., and Smith, A. F. M. (1990), "Sampling-Based Approaches to Calculating Marginal Densities," Journal of the American Statistical Association, 85, 398-409.
17. Glasbey, C. A., and Ghazal, P. (2003), "Combinatorial Image Analysis of DNA Microarray Features," Bioinformatics, 19, 194-203.
18. Gottardo, R., Pannucci, J. A., Kuske, C. R., and Brettin, T. (2003), "Statistical Analysis of Microarray Data: A Bayesian Approach," Biostatistics, 4, 597-620.
19. Huber, W., von Heydebreck, A., Sultmann, H., Poustka, A., and Vingron, M. (2002), "Variance Stabilization Applied to Microarray Data Calibration and to the Quantification of Differential Expression," Bioinformatics, 18, S96-S104.
20. Ideker, T., Thorsson, V., Siegel, A. F., and Hood, L. E. (2000), "Testing for Differentially Expressed Genes by Maximum-Likelihood Analysis of Microarray Data," Journal of Computational Biology, 7, 805-817.
21. Kerr, M. K., and Churchill, G. A. (2001), "Experimental Design for Gene Expression Microarrays," Biostatistics, 2, 183-201.
22. Kerr, M. K., Martin, M., and Churchill, G. (2000), "Analysis of Variance for Gene Expression Microarray Data," Journal of Computational Biology, 7, 819-837.
23. Lewin, A., Richardson, S., Marshall, C., Glazier, A., and Aitman, T. (2003). "Bayesian Modelling of Differential Gene Expression," technical report, Imperial College, London.
24. Li, C., and Wong, W. H. (2000), "Model-Based Analysis of Oligonucleotide Arrays: Expression Index Computation and Outlier Detection," Proceedings of the National Academy of Science USA, 98, 31-36.
25. Lindley, D. V., and Smith, A. F. M. (1972), "Bayes Estimates for the Linear Model," Journal of the Royal Statistical Society, Ser. B, 34, 1-41.
26. Lönnstedt, I., and Speed, T. P. (2002), "Replicated Microarray Data," Statistica Sinica, 12, 31-46.
27. Neal, R. (2003), "Slice Sampling," The Annals of Statistics, 31, 705-767.
28. 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, 37-52.
29. Newton, M. A., Noueiry, A., Sarkar, D., and Ahlquist, P. (2004), "Detecting Differential Gene Expression With a Semiparametric Hierarchical Mixture Method," Biostatistics, 5, 155-176.
30. Raftery, A. E., and Lewis, S. M. (1992), "How Many Iterations in the Gibbs Sampler?" in Bayesian Statistics 4, eds. J. M. Bernardo, J. O. Berger, A. P. Dawid, and A. F. M. Smith, Oxford, U.K.: Oxford University Press, pp. 763-773.
31. _ (1996), "Implementing MCMC," in Markov Chain Monte Carlo in Practice, eds. W. R. Gilks, S. Richardson, and D. J. Spiegelhalter, London: Chapman & Hall, pp. 115-130.
32. Rocke, D. M., and Durbin, B. (2001), "A Model for Measurement Error for Gene Expression Arrays," Journal of Computational Biology, 8, 557-569.
33. _ (2003), "Approximate Variance-Stabilizing Transformations for Gene-Expression Microarray Data," Bioinformatics, 19, 966-972.
34. Schena, M., Shalon, D., Davis, R. W., and Brown, P. (1995), "Quantitative Monitoring of Gene-Expression Patterns With a Complementary-DNA Microarray," Science, 270, 467-470.
35. Stephens, M. (2000), "Dealing With Label-Switching in Mixture Models," Journal of the Royal Statistical Society, Ser. B, 62, 795-809.
36. Tseng, G. C., Oh, M., Rohlin, L., Liao, J. C., and Wong, W. H. (2001), "Issues in cDNA Microarray Analysis: Quality Filtering, Channel Normalization, Models of Variations and Assessment of Gene Effects," Nucleic Acid Research, 29, 2549-2557.
37. Tukey, J. W. (1957), "On the Comparative Anatomy of Transformations," The Annals of Mathematical Statistics, 28, 602-632.
38. + T-Cell Lines," Journal of Virology, 77, 1392-1402.
39. Vines, S. K., Gilks, W. R., and Wild, P. (1996), "Fitting Bayesian Multiple Random Effects Models," Statistics and Computing, 6, 337-346.
40. Yang, G. P., Ross, D. T., Kuang, W. W., Brown, P. O., and Weigel, R. J. (1999), "Combining SSH and cDNA Microarrays for Rapid Identification of Differentially Expressed Genes," Nucleic Acid Research, 27, 1517-1523.
41. Yang, Y. H., Buckley, M. J., Dudoit, S., and Speed, T. P. (2002a), "Comparison of Methods for Image Analysis on cDNA Microarray Data," Journal of Computational and Graphical Statistics, 11, 108-136.
42. Yang, Y. H., Dudoit, S., Luu, P., Lin, D. M., Peng, V., Ngai, J., and Speed, T. P. (2002b), "Normalization for cDNA Microarray Data: A Robust Composite Method Addressing Single and Multiple Slide Systematic Variation," Nucleic Acids Research, 30, e15.