Bayesian variable selection for probit mixed models applied to gene selection

DOI10.1214/11-BA607MaRDI QIDQ2634086zbMATH OpenFDO

Authors Meli Baragatti

Publication date 8 February 2016

Published in Bayesian Analysis (Search for Journal in Brave)

Full work available at URL https://arxiv.org/abs/1101.4577, https://projecteuclid.org/euclid.ba/1339612044

zbMATH Keywords

Bayesian variable selectiongrouping technique (or blocking technique)Metropolis-within-Gibbs algorithmprobit mixed regression modelrandom effects

Mathematics Subject Classification ID

Bayesian inference (62F15) Ridge regression; shrinkage estimators (Lasso) (62J07) Generalized linear models (logistic models) (62J12) Applications of statistics to biology and medical sciences; meta analysis (62P10) Genetics and epigenetics (92D10)

Abstract: In computational biology, gene expression datasets are characterized by very few individual samples compared to a large number of measurements per sample. Thus, it is appealing to merge these datasets in order to increase the number of observations and diversify the data, allowing a more reliable selection of genes relevant to the biological problem. Besides, the increased size of a merged dataset facilitates its re-splitting into training and validation sets. This necessitates the introduction of the dataset as a random effect. In this context, extending a work of Lee et al. (2003), a method is proposed to select relevant variables among tens of thousands in a probit mixed regression model, considered as part of a larger hierarchical Bayesian model. Latent variables are used to identify subsets of selected variables and the grouping (or blocking) technique of Liu (1994) is combined with a Metropolis-within-Gibbs algorithm (Robert and Casella 2004). The method is applied to a merged dataset made of three individual gene expression datasets, in which tens of thousands of measurements are available for each of several hundred human breast cancer samples. Even for this large dataset comprised of around 20000 predictors, the method is shown to be efficient and feasible. As an illustration, it is used to select the most important genes that characterize the estrogen receptor status of patients with breast cancer.

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(11)

• Convergence analysis of the block Gibbs sampler for Bayesian probit linear mixed models with improper priors
• Theory of optimal Bayesian feature filtering
• Bayesian variable selection with sparse and correlation priors for high-dimensional data analysis
• Bayesian Variable Selections for Probit Models with Componentwise Gibbs Samplers
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• A study of variable selection using \(g\)-prior distribution with ridge parameter
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• Bayesian Model Averaging: A Systematic Review and Conceptual Classification
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