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The International Journal of Biostatistics

Ed. by Chambaz, Antoine / Hubbard, Alan E. / van der Laan, Mark J.

IMPACT FACTOR 2018: 1.309

CiteScore 2018: 1.11

SCImago Journal Rank (SJR) 2018: 1.325
Source Normalized Impact per Paper (SNIP) 2018: 0.715

Mathematical Citation Quotient (MCQ) 2018: 0.03

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A Marginal Mixture Model for Selecting Differentially Expressed Genes across Two Types of Tissue Samples

Weiliang Qiu / Wenqing He / Xiaogang Wang / Ross Lazarus
Published Online: 2008-10-09 | DOI: https://doi.org/10.2202/1557-4679.1093

Bayesian hierarchical models that characterize the distributions of (transformed) gene profiles have been proven very useful and flexible in selecting differentially expressed genes across different types of tissue samples (e.g. Lo and Gottardo, 2007). However, the marginal mean and variance of these models are assumed to be the same for different gene clusters and for different tissue types. Moreover, it is not easy to determine which of the many competing Bayesian hierarchical models provides the best fit for a specific microarray data set. To address these two issues, we propose a marginal mixture model that directly models the marginal distribution of transformed gene profiles. Specifically, we approximate the marginal distributions of transformed gene profiles via a mixture of three-component multivariate Normal distributions, each component of which has the same structures of marginal mean vector and covariance matrix as those for Bayesian hierarchical models, but the values can differ. Based on the proposed model, a method is derived to select genes differentially expressed across two types of tissue samples. The derived gene selection method performs well on a real microarray data set and consistently has the best performance (based on class agreement indices) compared with several other gene selection methods on simulated microarray data sets generated from three different mixture models.

Keywords: Box-Cox transformation; differentially expressed gene; EM algorithm; hierarchical structure; mixture models; posterior probability

About the article

Published Online: 2008-10-09

Citation Information: The International Journal of Biostatistics, Volume 4, Issue 1, ISSN (Online) 1557-4679, DOI: https://doi.org/10.2202/1557-4679.1093.

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