Microarrays, empirical Bayes and the two-groups model

DOI10.1214/07-STS236zbMath1327.62046arXiv0808.0572OpenAlexW3100378224WikidataQ55887561 ScholiaQ55887561MaRDI QIDQ900479

Efron, Bradley

Publication date: 22 December 2015

Published in: Statistical Science (Search for Journal in Brave)

Full work available at URL: https://arxiv.org/abs/0808.0572

zbMATH Keywords

false discovery ratessimultaneous testsempirical null

Mathematics Subject Classification ID

Empirical decision procedures; empirical Bayes procedures (62C12)

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Uses Software

• GSA

Cites Work

• Unnamed Item
• On testing the significance of sets of genes
• Using specially designed exponential families for density estimation
• Robbins, empirical Bayes and microarrays
• Multiple hypothesis testing in microarray experiments.
• The control of the false discovery rate in multiple testing under dependency.
• Size, power and false discovery rates
• Statistical methods for detecting stellar occultations by Kuiper Belt objects: the Taiwanese--American occultation survey
• Generalizations of the familywise error rate
• Significance analysis of microarrays applied to the ionizing radiation response
• The Efficiency of Logistic Regression Compared to Normal Discriminant Analysis
• Linear Models and Empirical Bayes Methods for Assessing Differential Expression in Microarray Experiments
• Empirical Bayes Analysis of a Microarray Experiment
• Importance of replication in microarray gene expression studies: Statistical methods and evidence from repetitive cDNA hybridizations
• Strong Control, Conservative Point Estimation and Simultaneous Conservative Consistency of False Discovery Rates: A Unified Approach
• A Direct Approach to False Discovery Rates
• A Statistical Framework for Expression-Based Molecular Classification in Cancer
• Correlation and Large-Scale Simultaneous Significance Testing
• Testing Statistical Hypotheses
• Estimating the Proportion of True Null Hypotheses, with application to DNA Microarray Data
• Bayesian Modeling of Differential Gene Expression
• Large-Scale Simultaneous Hypothesis Testing
• Detecting differential gene expression with a semiparametric hierarchical mixture method
• False Discovery Rate–Adjusted Multiple Confidence Intervals for Selected Parameters
• A Bayesian Mixture Model for Differential Gene Expression

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