Bayesian Robust Inference for Differential Gene Expression in Microarrays with Multiple Samples

DOI10.1111/j.1541-0420.2005.00397.xzbMath1099.62128OpenAlexW2115463832WikidataQ51945684 ScholiaQ51945684MaRDI QIDQ5473201

Ka Yee Yeung, Raphael Gottardo, Roger E Bumgarner, Adrian E. Raftery

Publication date: 20 June 2006

Published in: Biometrics (Search for Journal in Brave)

Full work available at URL: https://doi.org/10.1111/j.1541-0420.2005.00397.x

zbMATH Keywords

mixturedistributionempirical BayesMarkov chain Monte CarloheteroscedasticityoutlierBayesian hierarchical modelBonferroni adjustmentsingular distribution\(t\)-distributioncDNA microarraysaffymetrix

Mathematics Subject Classification ID

Applications of statistics to biology and medical sciences; meta analysis (62P10) Bayesian inference (62F15) Biochemistry, molecular biology (92C40) Numerical analysis or methods applied to Markov chains (65C40)

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Uses Software

• EBarrays

Cites Work

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• Multiple hypothesis testing in microarray experiments.
• Significance analysis of microarrays applied to the ionizing radiation response
• Identification of Differentially Expressed Genes in High-Density Oligonucleotide Arrays Accounting for the Quantification Limits of the Technology
• Sampling-Based Approaches to Calculating Marginal Densities
• Empirical Bayes Analysis of a Microarray Experiment
• Bayesian Models for Gene Expression With DNA Microarray Data
• Operating Characteristics and Extensions of the False Discovery Rate Procedure
• Bayesian Analysis of Agricultural Field Experiments
• Large-Scale Simultaneous Hypothesis Testing
• Statistical analysis of microarray data: a Bayesian approach
• Detecting differential gene expression with a semiparametric hierarchical mixture method