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)

Related Items (21)

Estimating Effect Sizes of Differentially Expressed Genes for Power and Sample-Size Assessments in Microarray Experiments ⋮ Robust hyperparameter estimation protects against hypervariable genes and improves power to detect differential expression ⋮ A modified two-sample t-test based on permutation method for large-scale data ⋮ Empirical Bayesian approach to testing multiple hypotheses with separate priors for left and right alternatives ⋮ BOPA: A Bayesian hierarchical model for outlier expression detection ⋮ Constructing confidence intervals for selected parameters ⋮ Optimal significance analysis of microarray data in a class of tests whose null statistic can be constructed ⋮ A Flexible and Powerful Bayesian Hierarchical Model for ChIP-Chip Experiments ⋮ A Bayesian measurement error model for two-channel cell-based RNAi data with replicates ⋮ Size, power and false discovery rates ⋮ Estimation and selection in high-dimensional genomic studies for developing molecular diagnostics ⋮ On Bayes decision rule for testing multiple hypotheses with non-symmetric alternatives ⋮ Testing multiple hypotheses with skewed alternatives ⋮ Mixture Modeling for Genome‐Wide Localization of Transcription Factors ⋮ Asymptotic behavior of RA-estimates in autoregressive 2D processes ⋮ Gaga: a parsimonious and flexible model for differential expression analysis ⋮ Bayesian testing of many hypotheses \(\times \) many genes: a study of sleep apnea ⋮ Tail Posterior Probability for Inference in Pairwise and Multiclass Gene Expression Data ⋮ Sample Size Calculations Based on Ranking and Selection in Microarray Experiments ⋮ On-line changepoint detection and parameter estimation with application to genomic data ⋮ Robust estimation for spatial autoregressive processes based on bounded innovation propagation representations

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

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