Bayesian testing of many hypotheses many genes: a study of sleep apnea
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Bayesian testing of many hypotheses \(\times \) many genes: a study of sleep apnea
Bayesian testing of many hypotheses \(\times \) many genes: a study of sleep apnea
Abstract: Substantial statistical research has recently been devoted to the analysis of large-scale microarray experiments which provide a measure of the simultaneous expression of thousands of genes in a particular condition. A typical goal is the comparison of gene expression between two conditions (e.g., diseased vs. nondiseased) to detect genes which show differential expression. Classical hypothesis testing procedures have been applied to this problem and more recent work has employed sophisticated models that allow for the sharing of information across genes. However, many recent gene expression studies have an experimental design with several conditions that requires an even more involved hypothesis testing approach. In this paper, we use a hierarchical Bayesian model to address the situation where there are many hypotheses that must be simultaneously tested for each gene. In addition to having many hypotheses within each gene, our analysis also addresses the more typical multiple comparison issue of testing many genes simultaneously. We illustrate our approach with an application to a study of genes involved in obstructive sleep apnea in humans.
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Cites work
- A Model-Based Background Adjustment for Oligonucleotide Expression Arrays
- A Unified Approach for Simultaneous Gene Clustering and Differential Expression Identification
- Bayesian Robust Inference for Differential Gene Expression in Microarrays with Multiple Samples
- Detecting differential gene expression with a semiparametric hierarchical mixture method
- Exploration, normalization, and summaries of high density oligonucleotide array probe level data
- scientific article; zbMATH DE number 3567782 (Why is no real title available?)
- scientific article; zbMATH DE number 3626409 (Why is no real title available?)
- Linear Models and Empirical Bayes Methods for Assessing Differential Expression in Microarray Experiments
- Statistical significance for genomewide studies
- Stochastic Relaxation, Gibbs Distributions, and the Bayesian Restoration of Images
Cited in
(7)- BOPA: A Bayesian hierarchical model for outlier expression detection
- Asymptotic theory of dependent Bayesian multiple testing procedures under possible model misspecification
- A compositional model to assess expression changes from single-cell RNA-seq data
- Bayesian analysis of multiple hypothesis testing with applications to microarray experiments
- Gamma-based clustering via ordered means with application to gene-expression analysis
- Empirical Bayes ranking and selection methods via semiparametric hierarchical mixture models in microarray studies
- The importance of distinct modeling strategies for gene and gene-specific treatment effects in hierarchical models for microarray data
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