Abstract
For gene expression data we propose a hierarchical Bayesian method of analysis using latent variables, wherein we have combined normalization and classification in a single framework. The uncertainty associated with classification for each gene can also be estimated based on the posterior distributions of the latent variables applied. The proposed models are implemented using the MCMC algorithm.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Preview
Unable to display preview. Download preview PDF.
References
Baldi P, Long AD (2001) A Bayesian framework for the analysis of microarray expression data: regularized t-test and statistical inferences of gene changes. Bioinformatics 17: 509–519.
Best, N. G., Cowles, M. K. and Vines. S. K. (1995) CODA: Convergence Diagnosis and Output Analysis software for Gibbs Sampler output: Version 0.3. Cambridge: Medical Research Council Biostatistic Unit.
Dror RO, Murnick JG, Rinaldi NA (2002) A Bayesian approach to transcript estimation from gene array data: the BEAM technique. RECOMB 2002: Proceedings of the Sixth Annual International Conference on Research in Computational Molecular Biology (ACM PRESS).
Gelman A, Carlin JB, Stern HS, Rubin DB. (1995) Models for missing data. In: Bayesian data analysis. London: Chapman & Hall; pp. 439–66.
Geweke J. (1993) Bayesian treatment of the independent Student-t linear model. Journal of Applied Econometrics 8: S19–S40.
Gilks WR, Thomas A, Spiegelhalter DJ (1994) A language and program for complex Bayesian modeling. The Statistician 43: 169–178.
Green PJ. (1995) Reversible jump Markov Chain Monte Carlo computation and Bayesian model determination. Biometrika. 82: 711–732.
Ibrahim JG, Chen M-H, Gray RJ (2002) Bayesian models for gene expression with DNA microarray data. J Am Stat Assoc 97: 88–99.
Keller AD, Schummer M, Hood L, Ruzzo WL (2000) Bayesian classification of DNA array expression data, Technical Report, UW-CSE-2000-08-01, Dept. of Comp. Sc. & Engg., Univ. of Washington, Seattle.
Long AD, Mangalam HJ, Chan BY, Tolleri L, Hatfield GW, Baldi P (2001) Improved statistical inference from DNA microarray data using analysis of variance and a Bayesian statistical framework. J Biol Chem 276: 19937–19944.
Medvedovic M (2000) Identifying significant patterns of expression via Bayesian infinite mixture models. CAMDA’00: Critical Assessment of Techniques for Microarray Data Analysis, Duke University.
Medvedovic M and Sivaganesan S. (2002) Bayesian infinite mixture model based clustering of gene expression profiles. Bioinformatics 18: 1194–1206.
Newton MA, Kendziorski CM, Richmond CS, Blattner FR, Tsui KW (2001) On differential variability of expression ratios: improving statistical inference about gene expression changes from microarray data. J Comp Biol 8: 37–52.
Parmigiani G, Garrett ES, Anbazhagan R, Gabrielson E (2002) A statistical framework for expression-based molecular classification in cancer. J Roy Stat Soc B, 64: 717–736.
Pritchard CC, Hsu L, Delrow J, Nelson PS (2001) Project normal: Defining normal variance in mouse gene expression. Proc Natl Acad Sci USA 98: 13266–13271.
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2004 Springer Science + Business Media, Inc.
About this chapter
Cite this chapter
Bhattacharjee, M., Pritchard, C., Sillanpää, M.J., Arjas, E. (2004). Bayesian Characterization of Natural Variation in Gene Expression. In: Johnson, K.F., Lin, S.M. (eds) Methods of Microarray Data Analysis III. Springer, Boston, MA. https://doi.org/10.1007/0-306-48354-8_11
Download citation
DOI: https://doi.org/10.1007/0-306-48354-8_11
Publisher Name: Springer, Boston, MA
Print ISBN: 978-1-4020-7582-7
Online ISBN: 978-0-306-48354-7
eBook Packages: Springer Book Archive