Empirical Bayes Analysis of a Microarray Experiment

DOI10.1198/016214501753382129zbMATH Open1073.62511OpenAlexW2074089196WikidataQ58618328 ScholiaQ58618328MaRDI QIDQ4468321FDOQ4468321

Bradley Efron, Robert Tibshirani, John D. Storey, Virginia Goss Tusher

Publication date: 10 June 2004

Published in: Journal of the American Statistical Association (Search for Journal in Brave)

Full work available at URL: http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.331.3404

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Mathematics Subject Classification ID

Applications of statistics to biology and medical sciences; meta analysis (62P10) Biochemistry, molecular biology (92C40) Empirical decision procedures; empirical Bayes procedures (62C12)

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• A robust unified approach to analyzing methylation and gene expression data
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• A new perspective on robust \(M\)-estimation: finite sample theory and applications to dependence-adjusted multiple testing
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• An empirical Bayes testing procedure for detecting variants in analysis of next generation sequencing data
• Generalized estimating equations by considering additive terms for analyzing time-course gene sets data
• Adjusted regularization in latent graphical models: application to multiple-neuron spike count data
• Adjusted regularization of cortical covariance
• Order thresholding
• Bayesian growth curve model useful for high-dimensional longitudinal data
• Detecting Strong Signals in Gene Perturbation Experiments: An Adaptive Approach With Power Guarantee and FDR Control
• Cross-Dimensional Inference of Dependent High-Dimensional Data
• Robust Semiparametric Microarray Normalization and Significance Analysis
• Confidence distributions and empirical Bayes posterior distributions unified as distributions of evidential support
• A geometric interpretation of the permutation \(p\)-value and its application in eQTL studies
• Frequentist properties of Bayesian multiplicity control for multiple testing of normal means
• Bayesian variable selection in clustering high-dimensional data with substructure
• Diverse correlation structures in gene expression data and their utility in improving statistical inference
• An Efficient Morris Method-Based Framework for Simulation Factor Screening
• A powerful procedure that controls the false discovery rate with directional information
• A parametric model to estimate the proportion from true null using a distribution for \(p\)-values
• Adjusting background noise in cluster analyses of longitudinal data
• On the development of a local FDR-based approach to testing two-way classified hypotheses
• Modeling Microarray Data Using a Threshold Mixture Model
• Detecting differentially expressed genes by relative entropy
• Local false discovery rate based methods for multiple testing of one-way classified hypotheses
• Optimal significance analysis of microarray data in a class of tests whose null statistic can be constructed
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• Covariate-adjusted multiple testing in genome-wide association studies via factorial hidden Markov models
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• Identifying temporally differentially expressed genes through functional principal components analysis
• Hierarchical Bayesian meta-analysis models for cross-platform microarray studies
• Parametric and Nonparametric FDR Estimation Revisited
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• A simple yet efficient method of local false discovery rate estimation designed for genome-wide association data analysis
• Randomization Tests for Small Samples: An Application for Genetic Expression Data
• Shrunken p‐Values for Assessing Differential Expression with Applications to Genomic Data Analysis
• A probabilistic framework for microarray data analysis: fundamental probability models and statistical inference
• Bayesian nonparametric multiple testing
• Genome-wide significance levels and weighted hypothesis testing
• Game-theoretic probability combination with applications to resolving conflicts between statistical methods
• A cross-validation based estimation of the proportion of true null hypotheses
• A review of modern multiple hypothesis testing, with particular attention to the false discovery proportion
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• Detection boundary and higher criticism approach for rare and weak genetic effects
• Nonparametric Bayesian Estimation of Positive False Discovery Rates
• Semiparametric Regression of Multidimensional Genetic Pathway Data: Least‐Squares Kernel Machines and Linear Mixed Models
• New multiple testing method under no dependency assumption, with application to multiple comparisons problem
• Microarrays, empirical Bayes and the two-groups model
• Robust test for detecting a signal in a high dimensional sparse normal vector
• Empirical Bayes analysis of RNA sequencing experiments with auxiliary information
• An empirical Bayes mixture method for effect size and false discovery rate estimation
• A stochastic process approach to false discovery control.
• Ridge estimation of inverse covariance matrices from high-dimensional data
• Empirical null and false discovery rate inference for exponential families
• An adaptively weighted statistic for detecting differential gene expression when combining multiple transcriptomic studies
• Powerful multiple testing of paired null hypotheses using a latent graph model
• Asymptotic Bayes-optimality under sparsity of some multiple testing procedures
• The Clustering of Regression Models Method with Applications in Gene Expression Data
• Detecting mutations in mixed sample sequencing data using empirical Bayes
• Bayesian decision theoretic approach to hypothesis problems with skewed alternatives
• Empirical Bayes Confidence Intervals for Means of Natural Exponential Family‐Quadratic Variance Function Distributions with Application to Small Area Estimation
• Optimal rates of convergence for estimating the null density and proportion of nonnull effects in large-scale multiple testing
• A method for modifying multiple testing procedures
• The positive false discovery rate: A Bayesian interpretation and the \(q\)-value
• Optimal weighting for false discovery rate control
• Estimation of the proportion of true null hypotheses in high-dimensional data under dependence
• Properties of higher criticism under strong dependence
• Adapting to unknown sparsity by controlling the false discovery rate
• FDR-controlling stepwise procedures and their false negatives rates
• Optimal rank-based testing for principal components
• False discovery rate for functional data
• Stochastic approximation and Newton's estimate of a mixing distribution
• An exploration of aspects of Bayesian multiple testing
• Decision theory results for one-sided multiple comparison procedures
• Approaches to multiplicity issues in complex research in microarray analysis
• Exact calculations for false discovery proportion with application to least favorable configura\-tions
• Compound decision theory and empirical Bayes methods
• Operating Characteristics and Extensions of the False Discovery Rate Procedure
• Large-scale multiple testing under dependence
• Multiple hypothesis testing on composite nulls using constrained \(p\)-values
• Size, power and false discovery rates
• False discovery rate analysis of brain diffusion direction maps
• Bayesian state space models for dynamic genetic network construction across multiple tissues
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• A nonparametric mixture approach to density and null proportion estimation in large‐scale multiple comparison problems
• Significance analysis of microarrays applied to the ionizing radiation response
• Multiple testing with heterogeneous multinomial distributions
• Simple estimators of false discovery rates given as few as one or two \(p\)-values without strong parametric assumptions

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