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)

Cited In (only showing first 100 items - show all)

• 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
• More powerful control of the false discovery rate under dependence
• 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
• Multiple hypothesis testing in microarray experiments.
• 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
• Proportion of Non-Zero Normal Means: Universal Oracle Equivalences and Uniformly Consistent Estimators
• A Bayesian Mixture Model for Differential Gene Expression
• Tilting methods for assessing the influence of components in a classifier
• Genomic outlier profile analysis: mixture models, null hypotheses, and nonparametric estimation
• False Discovery Rate Smoothing
• Estimating the Null Distribution to Adjust Observed Confidence Levels for Genome-Scale Screening
• Bayesian Robust Inference for Differential Gene Expression in Microarrays with Multiple Samples
• Simultaneous and selective inference: Current successes and future challenges
• Mutual fund performance: false discoveries, bias, and power
• A new approach to multiple testing of grouped hypotheses
• Unsupervised empirical Bayesian multiple testing with external covariates
• A penalized matrix decomposition, with applications to sparse principal components and canonical correlation analysis
• New procedures controlling the false discovery proportion via Romano-Wolf's heuristic
• RandomisedP-values and nonparametric procedures in multiple testing
• Covariate-Assisted Ranking and Screening for Large-Scale Two-Sample Inference
• A Direct Approach to False Discovery Rates
• Power-enhanced multiple decision functions controlling family-wise error and false discovery rates
• A new class of mixture models for differential gene expression in DNA microarray data
• Mixture Model on the Variance for the Differential Analysis of Gene Expression Data
• Joint adaptive mean-variance regularization and variance stabilization of high dimensional data
• Simultaneous critical values for \(t\)-tests in very high dimensions
• Strong Control, Conservative Point Estimation and Simultaneous Conservative Consistency of False Discovery Rates: A Unified Approach
• Statistical significance for genomewide studies
• Multiple testing and error control in Gaussian graphical model selection
• Comment
• Robbins, empirical Bayes and microarrays
• Laplace approximated EM microarray analysis: an empirical Bayes approach for comparative microarray experiments
• Bayesian Error‐in‐Variable Survival Model for the Analysis of GeneChip Arrays
• Global testing under sparse alternatives: ANOVA, multiple comparisons and the higher criticism
• Statistical Methods for Expression Quantitative Trait Loci (eQTL) Mapping
• Kernel Knockoffs Selection for Nonparametric Additive Models
• A Simple Diagnostic Plot Connecting Robust Estimation, Outlier Detection, and False Discovery Rates
• False Discovery Rate Control Under General Dependence By Symmetrized Data Aggregation
• Higher criticism for large-scale inference, especially for rare and weak effects
• Dynamic adaptive multiple tests with finite sample FDR control
• A Modified False Discovery Rate Multiple-Comparisons Procedure for Discrete Data, Applied to Human Immunodeficiency Virus Genetics
• A new multiple testing method in the dependent case
• Probabilistic inference for multiple testing
• Resampling-based multiple testing for microarray data analysis (With comments)
• Multiple Testing of Composite Null Hypotheses in Heteroscedastic Models
• Transformations, background estimation, and process effects in the statistical analysis of microarrays
• Stable classification with applications to microarray data
• Multiple testing for exploratory research
• A new efficient statistical test for detecting variability in the gene expression data
• Cluster analysis using multivariate normal mixture models to detect differential gene expression with microarray data
• A high-dimensional two-sample test for the mean using random subspaces
• On the performance of FDR control: constraints and a partial solution
• A nested mixture model for protein identification using mass spectrometry
• Comparison of various statistical methods for identifying differential gene expression in replicated microarray data
• Multiple testing on standardized mortality ratios: a Bayesian hierarchical model for FDR estimation

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