Empirical Bayes Analysis of a Microarray Experiment

DOI10.1198/016214501753382129zbMath1073.62511OpenAlexW2074089196WikidataQ58618328 ScholiaQ58618328MaRDI QIDQ4468321

John D. Storey, Efron, Bradley, Robert Tibshirani, 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

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)

Related Items

The influence of misspecified covariance on false discovery control when using posterior probabilities, Large-Scale Hypothesis Testing for Causal Mediation Effects with Applications in Genome-wide Epigenetic Studies, Detection of Local Differences in Spatial Characteristics Between Two Spatiotemporal Random Fields, Confidence Intervals for Nonparametric Empirical Bayes Analysis, LAWS: A Locally Adaptive Weighting and Screening Approach to Spatial Multiple Testing, Heteroscedasticity-Adjusted Ranking and Thresholding for Large-Scale Multiple Testing, Multiple testing with heterogeneous multinomial distributions, Shrunken p‐Values for Assessing Differential Expression with Applications to Genomic Data Analysis, Null Hypothesis Significance Testing Interpreted and Calibrated by Estimating Probabilities of Sign Errors: A Bayes-Frequentist Continuum, Statistical significance for genomewide studies, On the d-posterior approach to the multiple testing problem, Confidence distributions and empirical Bayes posterior distributions unified as distributions of evidential support, Empirical Bayes Confidence Intervals for Means of Natural Exponential Family‐Quadratic Variance Function Distributions with Application to Small Area Estimation, A modified two-sample t-test based on permutation method for large-scale data, A powerful procedure that controls the false discovery rate with directional information, Distributed eQTL analysis with auxiliary information, Efficient detection and classification of epigenomic changes under multiple conditions, Optimal Multiple Testing and Design in Clinical Trials, A nonparametric mixture approach to density and null proportion estimation in large‐scale multiple comparison problems, Double Empirical Bayes Testing, Fiducialize statistical significance: transformingp-values into conservative posterior probabilities and Bayes factors, Regularized t$$ t $$ distribution: definition, properties, and applications, False Discovery Rate Control via Data Splitting, Replicability across multiple studies, Bayesian variable selection using Knockoffs with applications to genomics, Adaptive novelty detection with false discovery rate guarantee, What is a Randomization Test?, Sequential tests of multiple hypotheses controlling false discovery and nondiscovery rates, Maximum likelihood estimation of the log-concave component in a semi-parametric mixture with a standard normal density, Hierarchical Bayesian meta-analysis models for cross-platform microarray studies, Evaluation of false discovery rate and power via sample size in microarray studies, Application of skew-normal distribution for detecting differential expression to microRNA data, Identification of genomic markers correlated with sensitivity in solid tumors to Dasatinib using sparse principal components, An Efficient Morris Method-Based Framework for Simulation Factor Screening, Detecting Strong Signals in Gene Perturbation Experiments: An Adaptive Approach With Power Guarantee and FDR Control, Bayesian Error‐in‐Variable Survival Model for the Analysis of GeneChip Arrays, A multiple testing protocol for exploratory data analysis and the local misclassification rate, Multiple testing using the posterior probabilities of directional alternatives, with application to genomic studies, Large‐scale signal detection: A unified perspective, Assessing Differential Gene Expression with Small Sample Sizes in Oligonucleotide Arrays Using a Mean‐Variance Model, Positive False Discovery Rate Estimate in Step-Wise Variable Selection, Mixture Model on the Variance for the Differential Analysis of Gene Expression Data, A Modified False Discovery Rate Multiple-Comparisons Procedure for Discrete Data, Applied to Human Immunodeficiency Virus Genetics, A Bayesian Mixture Model for Differential Gene Expression, Semiparametric Regression of Multidimensional Genetic Pathway Data: Least‐Squares Kernel Machines and Linear Mixed Models, Nonparametric Bayesian Estimation of Positive False Discovery Rates, On empirical distribution function of high-dimensional Gaussian vector components with an application to multiple testing, Multiple testing for exploratory research, Searching for differential expression: a non-parametric approach, Local comparison of empirical distributions via nonparametric regression, Bayesian Modeling of Differential Gene Expression, Bayesian Robust Inference for Differential Gene Expression in Microarrays with Multiple Samples, Statistical Methods for Expression Quantitative Trait Loci (eQTL) Mapping, On the Screening of Large Numbers of Significance Tests, Spatially Dependent Multiple Testing Under Model Misspecification, With Application to Detection of Anthropogenic Influence on Extreme Climate Events, Covariate-Assisted Ranking and Screening for Large-Scale Two-Sample Inference, The Clustering of Regression Models Method with Applications in Gene Expression Data, Functional Hierarchical Models for Identifying Genes with Different Time‐Course Expression Profiles, Robust Semiparametric Microarray Normalization and Significance Analysis, A Statistical Procedure for Detecting Highly Correlated Genes with a Pre-Specified Candidate Gene in Microarray Analysis, Unnamed Item, Interval estimation, point estimation, and null hypothesis significance testing calibrated by an estimated posterior probability of the null hypothesis, False discovery rate control for grouped or discretely supported p-values with application to a neuroimaging study, Where to find needles in a haystack?, Null-free false discovery rate control using decoy permutations, A stochastic process approach to false discovery control., Generalized estimating equations by considering additive terms for analyzing time-course gene sets data, A high-dimensional two-sample test for the mean using random subspaces, Adjusted regularization in latent graphical models: application to multiple-neuron spike count data, Adjusted regularization of cortical covariance, FDR-controlling stepwise procedures and their false negatives rates, Bayesian state space models for dynamic genetic network construction across multiple tissues, Comments on: Optimization and data mining in medicine, Optimal rates of convergence for estimating the null density and proportion of nonnull effects in large-scale multiple testing, A new approach to multiple testing of grouped hypotheses, Estimation of the proportion of true null hypotheses in high-dimensional data under dependence, 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, Ridge estimation of inverse covariance matrices from high-dimensional data, Bayesian nonparametric multiple testing, Simultaneous estimation based on empirical likelihood and general maximum likelihood estimation, A multivariate empirical Bayes statistic for replicated microarray time course data, Detection boundary and higher criticism approach for rare and weak genetic effects, Optimal rank-based testing for principal components, Optimal significance analysis of microarray data in a class of tests whose null statistic can be constructed, Inference after checking multiple Bayesian models for data conflict and applications to mitigating the influence of rejected priors, Microarrays, empirical Bayes and the two-groups model, Comment: ``Microarrays, empirical Bayes and the two-group model, Dynamic adaptive multiple tests with finite sample FDR control, A method for modifying multiple testing procedures, Laplace approximated EM microarray analysis: an empirical Bayes approach for comparative microarray experiments, Interval estimation for messy observational data, Genome-wide significance levels and weighted hypothesis testing, Stochastic approximation and Newton's estimate of a mixing distribution, Nonparametric density estimation for symmetric distributions by contaminated data, Robust test for detecting a signal in a high dimensional sparse normal vector, Simultaneous critical values for \(t\)-tests in very high dimensions, Asymptotic Bayes-optimality under sparsity of some multiple testing procedures, False discovery rate control with multivariate \(p\)-values, The false discovery rate for statistical pattern recognition, Optimal weighting for false discovery rate control, Multiple hypothesis testing on composite nulls using constrained \(p\)-values, False discovery rates in somatic mutation studies of cancer, An adaptively weighted statistic for detecting differential gene expression when combining multiple transcriptomic studies, Deriving and comparing the distribution for the number of false positives in single step methods to control \(k\)-FWER, Game-theoretic probability combination with applications to resolving conflicts between statistical methods, Multiple testing and error control in Gaussian graphical model selection, Mutual fund performance: false discoveries, bias, and power, Robust semiparametric optimal testing procedure for multiple normal means, A probabilistic framework for microarray data analysis: fundamental probability models and statistical inference, Resampling-based multiple testing for microarray data analysis (With comments), Single-index modulated multiple testing, Robbins, empirical Bayes and microarrays, Compound decision theory and empirical Bayes methods, The positive false discovery rate: A Bayesian interpretation and the \(q\)-value, Statistical challenges in functional genomics. (With comments and a rejoinder)., Multiple hypothesis testing in microarray experiments., An extension of the \(K\)-means algorithm to clustering skewed data, Global testing under sparse alternatives: ANOVA, multiple comparisons and the higher criticism, An optimal procedure for multiple hypotheses testing, Clustering gene expression profile data by selective shrinkage, A look at multiplicity through misclassification, Frequentist-Bayesian Monte Carlo test for mean vectors in high dimension, Transformations, background estimation, and process effects in the statistical analysis of microarrays, Stable classification with applications to microarray data, A two-stage empirical Bayes method for identifying differentially expressed genes, A mixture model approach for the analysis of small exploratory microarray experiments, Assumption adequacy averaging as a concept for developing more robust methods for differential gene expression analysis, Balancing type one and two errors in multiple testing for differential expression of genes, A robust unified approach to analyzing methylation and gene expression data, A flexible approximate likelihood ratio test for detecting differential expression in microarray data, Joint adaptive mean-variance regularization and variance stabilization of high dimensional data, Empirical Bayes analysis of unreplicated microarray data, A penalized matrix decomposition, with applications to sparse principal components and canonical correlation analysis, Sample size calculation for a regularized \(t\)-statistic in microarray experiments, Sequential prediction bounds for identifying differentially expressed genes in replicated microarray experiments, An empirical Bayes mixture method for effect size and false discovery rate estimation, MAOSA: A new procedure for detection of differential gene expression, Detecting mutations in mixed sample sequencing data using empirical Bayes, Bayesian decision theoretic approach to hypothesis problems with skewed alternatives, Decision theory results for one-sided multiple comparison procedures, Order thresholding, A cross-validation based estimation of the proportion of true null hypotheses, Kernel Knockoffs Selection for Nonparametric Additive Models, A nested mixture model for protein identification using mass spectrometry, A geometric interpretation of the permutation \(p\)-value and its application in eQTL studies, Empirical null and false discovery rate inference for exponential families, False Discovery Rate Control Under General Dependence By Symmetrized Data Aggregation, Distributions associated with simultaneous multiple hypothesis testing, A new perspective on robust \(M\)-estimation: finite sample theory and applications to dependence-adjusted multiple testing, On false discovery rate thresholding for classification under sparsity, Cluster analysis using multivariate normal mixture models to detect differential gene expression with microarray data, On the development of a local FDR-based approach to testing two-way classified hypotheses, A clarifying comparison of methods for controlling the false discovery rate, A new multiple testing method in the dependent case, A semi-parametric approach for mixture models: application to local false discovery rate estimation, A Bayesian approach for decision making on the identification of genes with different expression levels: an application to Escherichia coli bacterium data, More powerful control of the false discovery rate under dependence, A note on multiple testing for composite null hypotheses, Semi-supervised multiple testing, Local false discovery rate based methods for multiple testing of one-way classified hypotheses, Higher criticism for large-scale inference, especially for rare and weak effects, New multiple testing method under no dependency assumption, with application to multiple comparisons problem, Comment, Bayesian growth curve model useful for high-dimensional longitudinal data, A simple yet efficient method of local false discovery rate estimation designed for genome-wide association data analysis, Modeling Microarray Data Using a Threshold Mixture Model, Optimal false discovery rate control for large scale multiple testing with auxiliary information, False discovery rate control with unknown null distribution: is it possible to mimic the oracle?, An Empirical Bayes' Approach to Joint Analysis of Multiple Microarray Gene Expression Studies, An exploration of aspects of Bayesian multiple testing, Statistical Techniques for Microarray Data: A Partial Overview, Publication Policies for Replicable Research and the Community-Wide False Discovery Rate, Empirical Bayes cumulative \(\ell\)-value multiple testing procedure for sparse sequences, Powerful multiple testing of paired null hypotheses using a latent graph model, Improved Detection of Differentially Expressed Genes Through Incorporation of Gene Locations, Large-Scale Multiple Testing under Dependence, Tilting Methods for Assessing the Influence of Components in a Classifier, Decentralized nonparametric multiple testing, False Discovery Rate Smoothing, Weighted False Discovery Rate Control in Large-Scale Multiple Testing, The role of empirical Bayes methodology as a leading principle in modern medical statistics, Bayesian local false discovery rate for sparse count data with application to the discovery of hotspots in protein domains, Detection of two-way outliers in multivariate data and application to cheating detection in educational tests, Mixed directional false discovery rate control in multiple pairwise comparisons using weightedp-values, Strong consistency and asymptotic normality for quantities related to the Benjamini-Hochberg false discovery rate procedure, Covariate-adjusted multiple testing in genome-wide association studies via factorial hidden Markov models, False discovery rate for functional data, Prioritizing covariates in the planning of future studies in the meta-analytic framework, Detecting differentially expressed genes by relative entropy, Statistical proof? The problem of irreproducibility, Effects of statistical dependence on multiple testing under a hidden Markov model, Power-enhanced multiple decision functions controlling family-wise error and false discovery rates, Exact calculations for false discovery proportion with application to least favorable configura\-tions, Expected Power for the False Discovery Rate with Independence, Frequentist properties of Bayesian multiplicity control for multiple testing of normal means, A comprehensive error rate for multiple testing, Compound \(p\)-value statistics for multiple testing procedures, High-dimensional influence measure, An empirical Bayes testing procedure for detecting variants in analysis of next generation sequencing data, On spike and slab empirical Bayes multiple testing, Adaptive linear step-up multiple testing procedure with the bias-reduced estimator, Size, power and false discovery rates, On the performance of FDR control: constraints and a partial solution, An empirical Bayes change-point model for transcriptome time-course data, Multiple testing on standardized mortality ratios: a Bayesian hierarchical model for FDR estimation, Accurate genome-scale percentage DNA methylation estimates from microarray data, Genomic outlier profile analysis: mixture models, null hypotheses, and nonparametric estimation, Identifying temporally differentially expressed genes through functional principal components analysis, Bayesian ranking and selection methods using hierarchical mixture models in microarray studies, An empirical Bayes approach for the identification of long-range chromosomal interaction from Hi-C data, A statistical analysis of memory CD8 T cell differentiation: An application of a hierarchical state space model to a short time course microarray experiment, Diverse correlation structures in gene expression data and their utility in improving statistical inference, False discovery variance reduction in large scale simultaneous hypothesis tests, Adaptive nonparametric estimation of a component density in a two-class mixture model, Estimating the Null Distribution to Adjust Observed Confidence Levels for Genome-Scale Screening, Integrating Prior Knowledge in Multiple Testing under Dependence with Applications to Detecting Differential DNA Methylation, Bayesian Analysis of Multiple Hypothesis Testing with Applications to Microarray Experiments, The Positive False Discovery Quantile, Hadamard matrix methods in identifying differentially expressed genes from microarray experi\-ments, A new class of mixture models for differential gene expression in DNA microarray data, Properties of higher criticism under strong dependence, Cross-Dimensional Inference of Dependent High-Dimensional Data, Multiple Testing of Composite Null Hypotheses in Heteroscedastic Models, False discovery rate analysis of brain diffusion direction maps, Discovering focal regions of slightly-aggregated sparse signals, Bayesian variable selection in clustering high-dimensional data with substructure, Strong Control, Conservative Point Estimation and Simultaneous Conservative Consistency of False Discovery Rates: A Unified Approach, A Simple Procedure for the Selection of Significant Effects, A Direct Approach to False Discovery Rates, Operating Characteristics and Extensions of the False Discovery Rate Procedure, An Improved Method on Wilcoxon Rank Sum Test for Gene Selection from Microarray Experiments, A Statistical Framework for Expression-Based Molecular Classification in Cancer, False discovery and false nondiscovery rates in single-step multiple testing procedures, A Simple Diagnostic Plot Connecting Robust Estimation, Outlier Detection, and False Discovery Rates, The false discovery rate: a variable selection perspective, Unsupervised empirical Bayesian multiple testing with external covariates, Adapting to unknown sparsity by controlling the false discovery rate, The split sample permutation \(t\)-tests, A review of modern multiple hypothesis testing, with particular attention to the false discovery proportion, A new efficient statistical test for detecting variability in the gene expression data, Uniformly consistently estimating the proportion of false null hypotheses via Lebesgue-Stieltjes integral equations, A Robust Method for Large-Scale Multiple Hypotheses Testing, Spatial Boundary Detection for Areal Counts, Empirical Bayes analysis of RNA sequencing experiments with auxiliary information, Simultaneous and selective inference: Current successes and future challenges, DNA Microarray Experiments: Biological and Technological Aspects, Gene expression associations with the growth inhibitory effects of small molecules on live cells: Specificity of effects and uniformity of mechanisms, Proportion of Non-Zero Normal Means: Universal Oracle Equivalences and Uniformly Consistent Estimators, Data Volume and Power of Multiple Tests with Small Sample Size Per Null, RandomisedP-values and nonparametric procedures in multiple testing, A Comparison of Procedures for Controlling the False Discovery Rate in the Presence of Small Variance Genes: A Simulation Study, Dynamic adaptive procedures that control the false discovery rate, Approaches to multiplicity issues in complex research in microarray analysis, Comparison of various statistical methods for identifying differential gene expression in replicated microarray data, Inequalities for the false discovery rate (FDR) under dependence, A Decision‐Theory Approach to Interpretable Set Analysis for High‐Dimensional Data, Randomization Tests for Small Samples: An Application for Genetic Expression Data, Simple estimators of false discovery rates given as few as one or two \(p\)-values without strong parametric assumptions, Parametric and Nonparametric FDR Estimation Revisited, Bayesian tests for composite alternative hypotheses in cross-tabulated data, New procedures controlling the false discovery proportion via Romano-Wolf's heuristic, Probabilistic inference for multiple testing