Linear Models and Empirical Bayes Methods for Assessing Differential Expression in Microarray Experiments
From MaRDI portal
Publication:4459296
DOI10.2202/1544-6115.1027zbMath1038.62110OpenAlexW2081098333WikidataQ27860758 ScholiaQ27860758MaRDI QIDQ4459296
Publication date: 28 March 2004
Published in: Statistical Applications in Genetics and Molecular Biology (Search for Journal in Brave)
Full work available at URL: http://www.bepress.com/sagmb/vol3/iss1/art3/
Applications of statistics to biology and medical sciences; meta analysis (62P10) Biochemistry, molecular biology (92C40) Empirical decision procedures; empirical Bayes procedures (62C12)
Related Items (only showing first 100 items - show all)
Improved Small Domain Estimation via Compromise Regression Weights ⋮ Context-Specific Nested Effects Models ⋮ Bayesian growth curve model useful for high-dimensional longitudinal data ⋮ Incorporation of gene exchangeabilities improves the reproducibility of gene set rankings ⋮ Hierarchical Bayes variable selection and microarray experiments ⋮ A novel Chow-Liu algorithm and its application to gene differential analysis ⋮ A Unified Approach for Simultaneous Gene Clustering and Differential Expression Identification ⋮ Robust hyperparameter estimation protects against hypervariable genes and improves power to detect differential expression ⋮ A semi-parametric Bayesian approach for detection of gene expression heterosis with RNA-seq data ⋮ Adaptive Filtering Increases Power to Detect Differentially Expressed Genes ⋮ Tilting Methods for Assessing the Influence of Components in a Classifier ⋮ A multivariate empirical Bayes statistic for replicated microarray time course data ⋮ Rotation gene set testing for longitudinal expression data ⋮ Confidence distributions and empirical Bayes posterior distributions unified as distributions of evidential support ⋮ High dimensional extension of the growth curve model and its application in genetics ⋮ Empirical Bayes Confidence Intervals for Selected Parameters in High-Dimensional Data ⋮ Discrimination and scoring using small sets of genes for two-sample microarray data ⋮ No counts, no variance: allowing for loss of degrees of freedom when assessing biological variability from RNA-seq data ⋮ Statistical inferences based on outliers for gene expression analysis ⋮ Fitting very large sparse Gaussian graphical models ⋮ BOPA: A Bayesian hierarchical model for outlier expression detection ⋮ Gamma-based clustering via ordered means with application to gene-expression analysis ⋮ A statistical framework for non-negative matrix factorization based on generalized dual divergence ⋮ James-Stein type estimators of variances ⋮ \texttt{EBADIMEX}: an empirical Bayes approach to detect joint differential expression and methylation and to classify samples ⋮ Regularized t$$ t $$ distribution: definition, properties, and applications ⋮ Microarrays, empirical Bayes and the two-groups model ⋮ Co-clustering of spatially resolved transcriptomic data ⋮ Empirical Bayes Mean Estimation With Nonparametric Errors Via Order Statistic Regression on Replicated Data ⋮ Laplace approximated EM microarray analysis: an empirical Bayes approach for comparative microarray experiments ⋮ A Hilbert Space Embedding for Distributions ⋮ A Bayesian model averaging approach for observational gene expression studies ⋮ An adaptively weighted statistic for detecting differential gene expression when combining multiple transcriptomic studies ⋮ The changing focus of microarray analysis ⋮ Evaluation of Laplace distribution-based ANOVA models applied to microarray data ⋮ Empirical null distribution-based modeling of multi-class differential gene expression detection ⋮ A note on statistical method for genotype calling of high-throughput single-nucleotide polymorphism arrays ⋮ Robust semiparametric optimal testing procedure for multiple normal means ⋮ On a variance stabilizing model and its application to genomic data ⋮ Unnamed Item ⋮ Application of skew-normal distribution for detecting differential expression to microRNA data ⋮ Applying shrinkage variance estimators to the TOST test in high dimensional settings ⋮ Prediction of key transcription factors during skin regeneration by combining gene expression data and regulatory network information analysis ⋮ Bayesian identification of protein differential expression in multi-group isobaric labelled mass spectrometry data ⋮ Hommel's procedure in linear time ⋮ Identification of genomic markers correlated with sensitivity in solid tumors to Dasatinib using sparse principal components ⋮ Estimating the number of genes that are differentially expressed in both of two independent experiments ⋮ Empirical Bayes Confidence Intervals Shrinking Both Means and Variances ⋮ Estimation and testing of gene expression heterosis ⋮ Optimal designs for 2-color microarray experiments ⋮ A hidden Markov random field model for genome-wide association studies ⋮ Optimal screening for promising genes in 2-stage designs ⋮ Modified test statistics by inter-voxel variance shrinkage with an application to f MRI ⋮ Microarray background correction: maximum likelihood estimation for the normal-exponential convolution ⋮ Variable importance assessments and backward variable selection for multi-sample problems ⋮ A statistical framework for the analysis of microarray probe-level data ⋮ Unifying and Generalizing Methods for Removing Unwanted Variation Based on Negative Controls ⋮ Use of pretransformation to cope with extreme values in important candidate features ⋮ A Time‐Series DDP for Functional Proteomics Profiles ⋮ A Hierarchical Semiparametric Model for Incorporating Intergene Information for Analysis of Genomic Data ⋮ Improved Estimation of the Noncentrality Parameter Distribution from a Large Number of t‐Statistics, with Applications to False Discovery Rate Estimation in Microarray Data Analysis ⋮ Testing significance of features by lassoed principal components ⋮ A structural mixed model to shrink covariance matrices for time-course differential gene expression studies ⋮ Modified linear discriminant analysis approaches for classification of high-dimensional microarray 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 ⋮ Can matching improve the performance of boosting for identifying important genes in observational studies? ⋮ Simultaneous inference: when should hypothesis testing problems be combined? ⋮ Poisson–Tweedie mixed-effects model: A flexible approach for the analysis of longitudinal RNA-seq data ⋮ Multiclass classification of sarcomas using pathway based feature selection method ⋮ Benchmark for filter methods for feature selection in high-dimensional classification data ⋮ Sample size calculation for a regularized \(t\)-statistic in microarray experiments ⋮ An Improved Method on Wilcoxon Rank Sum Test for Gene Selection from Microarray Experiments ⋮ Assessing Differential Gene Expression with Small Sample Sizes in Oligonucleotide Arrays Using a Mean‐Variance Model ⋮ Contaminated normal modeling with application to microarray data analysis ⋮ Estimating the False Discovery Rate Using Nonparametric Deconvolution ⋮ The importance of distinct modeling strategies for gene and gene-specific treatment effects in hierarchical models for microarray data ⋮ A mixture factor model with applications to microarray data ⋮ Gaga: a parsimonious and flexible model for differential expression analysis ⋮ Bayesian testing of many hypotheses \(\times \) many genes: a study of sleep apnea ⋮ Tail Posterior Probability for Inference in Pairwise and Multiclass Gene Expression Data ⋮ A model selection criterion for model-based clustering of annotated gene expression data ⋮ ESTIMATING BAYESIAN NETWORKS FOR HIGH-DIMENSIONAL DATA WITH COMPLEX MEAN STRUCTURE AND RANDOM EFFECTS ⋮ Empirical Bayes analysis of RNA sequencing experiments with auxiliary information ⋮ Bayesian Modeling of ChIP-chip Data Through a High-Order Ising Model ⋮ Unnamed Item ⋮ AAPL: assessing association between p‐value lists ⋮ Empirical and fully Bayesian approaches for random effects models in microarray data analysis ⋮ Theory of optimal Bayesian feature filtering ⋮ 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 ⋮ Bayesian Gene Set Analysis for Identifying Significant Biological Pathways ⋮ Large-scale simultaneous testing using kernel density estimation ⋮ Detecting multiple replicating signals using adaptive filtering procedures ⋮ Comparison of various statistical methods for identifying differential gene expression in replicated microarray data ⋮ Flexible estimation of a semiparametric two-component mixture model with one parametric component ⋮ Smoothness of marginal log-linear parameterizations ⋮ A Decision‐Theory Approach to Interpretable Set Analysis for High‐Dimensional Data ⋮ Statistical properties of gene-gene correlations in omics experiments ⋮ Computational Biology: Toward Deciphering Gene Regulatory Information in Mammalian Genomes
This page was built for publication: Linear Models and Empirical Bayes Methods for Assessing Differential Expression in Microarray Experiments
