A Bayesian model averaging approach for observational gene expression studies
From MaRDI portal
Abstract: Identifying differentially expressed (DE) genes associated with a sample characteristic is the primary objective of many microarray studies. As more and more studies are carried out with observational rather than well controlled experimental samples, it becomes important to evaluate and properly control the impact of sample heterogeneity on DE gene finding. Typical methods for identifying DE genes require ranking all the genes according to a preselected statistic based on a single model for two or more group comparisons, with or without adjustment for other covariates. Such single model approaches unavoidably result in model misspecification, which can lead to increased error due to bias for some genes and reduced efficiency for the others. We evaluated the impact of model misspecification from such approaches on detecting DE genes and identified parameters that affect the magnitude of impact. To properly control for sample heterogeneity and to provide a flexible and coherent framework for identifying simultaneously DE genes associated with a single or multiple sample characteristics and/or their interactions, we proposed a Bayesian model averaging approach which corrects the model misspecification by averaging over model space formed by all relevant covariates. An empirical approach is suggested for specifying prior model probabilities. We demonstrated through simulated microarray data that this approach resulted in improved performance in DE gene identification compared to the single model approaches. The flexibility of this approach is demonstrated through our analysis of data from two observational microarray studies.
Recommendations
- Bayesian analysis of comparative microarray experiments by model averaging
- Bayesian Modeling of Differential Gene Expression
- A Bayesian Model for Cross-Study Differential Gene Expression
- Detecting Differentially Expressed Genes in Microarrays Using Bayesian Model Selection
- A Bayesian approach to assessing differential expression of microarray data
Cites work
- scientific article; zbMATH DE number 6114088 (Why is no real title available?)
- scientific article; zbMATH DE number 3716572 (Why is no real title available?)
- A Bayesian model averaging approach for observational gene expression studies
- A Direct Approach to False Discovery Rates
- Bayes Factors
- Bayes and empirical-Bayes multiplicity adjustment in the variable-selection problem
- Bayesian analysis of comparative microarray experiments by model averaging
- Bayesian methods to overcome the winner's curse in genetic studies
- Bayesian model averaging: A tutorial. (with comments and a rejoinder).
- Bayesian robust transformation and variable selection: A unified approach
- Detecting differential gene expression with a semiparametric hierarchical mixture method
- Linear Models and Empirical Bayes Methods for Assessing Differential Expression in Microarray Experiments
- Measuring statistical significance for full Bayesian methods in microarray analyses
- Microarrays, empirical Bayes and the two-groups model
- Mixtures of g Priors for Bayesian Variable Selection
- On testing the significance of sets of genes
- Statistical significance for genomewide studies
Cited in
(4)- A Bayesian Model for Cross-Study Differential Gene Expression
- A Bayesian model averaging approach for observational gene expression studies
- Development of a tissue augmented Bayesian model for expression quantitative trait loci analysis
- Bayesian–frequentist hybrid model with application to the analysis of gene copy number changes
This page was built for publication: A Bayesian model averaging approach for observational gene expression studies
Report a bug (only for logged in users!)Click here to report a bug for this page (MaRDI item Q439134)
