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)

• 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
• 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
• Diverse correlation structures in gene expression data and their utility in improving statistical inference
• 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
• A clarifying comparison of methods for controlling the false discovery rate
• False discovery rate control with multivariate \(p\)-values
• A look at multiplicity through misclassification
• False discovery and false nondiscovery rates in single-step multiple testing procedures
• Inequalities for the false discovery rate (FDR) under dependence
• Confidence Intervals for Nonparametric Empirical Bayes Analysis
• Clustering gene expression profile data by selective shrinkage
• Bayesian tests for composite alternative hypotheses in cross-tabulated data
• Assessing Differential Gene Expression with Small Sample Sizes in Oligonucleotide Arrays Using a Mean‐Variance Model
• Frequentist-Bayesian Monte Carlo test for mean vectors in high dimension
• Sample size calculation for a regularized \(t\)-statistic in microarray experiments
• 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

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