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)

• On empirical distribution function of high-dimensional Gaussian vector components with an application to multiple testing
• A two-stage empirical Bayes method for identifying differentially expressed genes
• A mixture model approach for the analysis of small exploratory microarray experiments
• A robust unified approach to analyzing methylation and gene expression data
• Cluster analysis using multivariate normal mixture models to detect differential gene expression with microarray data
• An extension of the \(K\)-means algorithm to clustering skewed data
• A new perspective on robust \(M\)-estimation: finite sample theory and applications to dependence-adjusted multiple testing
• A multiple testing protocol for exploratory data analysis and the local misclassification rate
• 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
• Empirical and fully Bayesian approaches for random effects models in microarray data analysis
• The split sample permutation \(t\)-tests
• The Positive False Discovery Quantile
• A note on multiple testing for composite null hypotheses
• Statistical Techniques for Microarray Data: A Partial Overview
• Sequential tests of multiple hypotheses controlling false discovery and nondiscovery rates
• Mixed directional false discovery rate control in multiple pairwise comparisons using weightedp-values
• The false discovery rate: a variable selection perspective
• Covariate-adjusted multiple testing in genome-wide association studies via factorial hidden Markov models
• Multiple testing using the posterior probabilities of directional alternatives, with application to genomic studies
• 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
• Semi-supervised multiple testing
• 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
• 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
• 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
• Bayesian ranking and selection methods using hierarchical mixture models in microarray studies
• A Statistical Framework for Expression-Based Molecular Classification in Cancer
• MAOSA: A new procedure for detection of differential gene expression
• Application of skew-normal distribution for detecting differential expression to microRNA data
• High-dimensional influence measure
• Statistical challenges in functional genomics. (With comments and a rejoinder).
• Functional Hierarchical Models for Identifying Genes with Different Time‐Course Expression Profiles
• Nonparametric density estimation for symmetric distributions by contaminated data
• Bayesian Analysis of Multiple Hypothesis Testing with Applications to Microarray Experiments
• Searching for differential expression: a non-parametric approach
• Distributions associated with simultaneous multiple hypothesis testing
• Comments on: Optimization and data mining in medicine
• Null Hypothesis Significance Testing Interpreted and Calibrated by Estimating Probabilities of Sign Errors: A Bayes-Frequentist Continuum
• Expected Power for the False Discovery Rate with Independence
• Robust semiparametric optimal testing procedure for multiple normal means
• Balancing type one and two errors in multiple testing for differential expression of genes
• A semi-parametric approach for mixture models: application to local false discovery rate estimation
• Simultaneous estimation based on empirical likelihood and general maximum likelihood estimation
• Compound \(p\)-value statistics for multiple testing procedures
• A flexible approximate likelihood ratio test for detecting differential expression in microarray data
• Single-index modulated multiple testing
• Bayesian Modeling of Differential Gene Expression
• On false discovery rate thresholding for classification under sparsity
• Integrating Prior Knowledge in Multiple Testing under Dependence with Applications to Detecting Differential DNA Methylation
• A multivariate empirical Bayes statistic for replicated microarray time course data
• Deriving and comparing the distribution for the number of false positives in single step methods to control \(k\)-FWER
• Empirical Bayes Microarray ANOVA and Grouping Cell Lines by Equal Expression Levels
• Empirical Bayes Estimation of a Sparse Vector of Gene Expression Changes
• A Bayesian approach for decision making on the identification of genes with different expression levels: an application to Escherichia coli bacterium data
• Inference after checking multiple Bayesian models for data conflict and applications to mitigating the influence of rejected priors
• Comment: ``Microarrays, empirical Bayes and the two-group model
• Assumption adequacy averaging as a concept for developing more robust methods for differential gene expression analysis
• Empirical Bayes analysis of unreplicated microarray 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
• Interval estimation for messy observational data
• Strong consistency and asymptotic normality for quantities related to the Benjamini-Hochberg false discovery rate procedure
• DNA Microarray Experiments: Biological and Technological Aspects
• False discovery rates in somatic mutation studies of cancer
• An optimal procedure for multiple hypotheses testing
• The false discovery rate for statistical pattern recognition
• Sequential prediction bounds for identifying differentially expressed genes in replicated microarray experiments

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