Replicability analysis for genome-wide association studies

DOI10.1214/13-aoas697zbMath1454.62340arXiv1209.2829OpenAlexW2042879443MaRDI QIDQ153020

Ruth Heller, Daniel Yekutieli, Daniel Yekutieli, Ruth Heller

Publication date: 1 March 2014

Published in: The Annals of Applied Statistics (Search for Journal in Brave)

Full work available at URL: https://arxiv.org/abs/1209.2829

zbMATH Keywords

empirical Bayesreplicationfalse discovery ratemeta-analysistype 2 diabetesreproducibilitycombined analysis

Mathematics Subject Classification ID

Applications of statistics to biology and medical sciences; meta analysis (62P10) Paired and multiple comparisons; multiple testing (62J15)

Related Items

False discovery rate control with unknown null distribution: is it possible to mimic the oracle? ⋮ Optimal detection of weak positive latent dependence between two sequences of multiple tests ⋮ Rejoinder on: ``Hierarchical inference for genome-wide association studies: a view on methodology with software ⋮ Distributed eQTL analysis with auxiliary information ⋮ Randomized ‐values for multiple testing and their application in replicability analysis ⋮ Testing partial conjunction hypotheses under dependency, with applications to meta-analysis ⋮ Replicability across multiple studies ⋮ Nonparametric false discovery rate control for identifying simultaneous signals ⋮ Replicability analysis for genome-wide association studies ⋮ repfdr ⋮ Admissibility in Partial Conjunction Testing ⋮ Covariate-Assisted Ranking and Screening for Large-Scale Two-Sample Inference ⋮ Semi-supervised multiple testing ⋮ Detecting multiple replicating signals using adaptive filtering procedures ⋮ Comments on: ``Hierarchical inference for genome-wide association studies: a view on methodology with software ⋮ Bayesian tests for composite alternative hypotheses in cross-tabulated data

Uses Software

• mixfdr
• fdrtool
• HAPGEN2

Cites Work

• Unnamed Item
• Unnamed Item
• Unnamed Item
• Unnamed Item
• Replicability analysis for genome-wide association studies
• Statistical tests for the intersection of independent lists of genes: sensitivity, FDR, and type I error control
• Microarrays, empirical Bayes and the two-groups model
• Replication in genome-wide association studies
• An empirical Bayes mixture method for effect size and false discovery rate estimation
• Karl Pearson's meta-analysis revisited
• The positive false discovery rate: A Bayesian interpretation and the \(q\)-value
• A note on pseudolikelihood constructed from marginal densities
• Adaptive linear step-up procedures that control the false discovery rate
• Screening for Partial Conjunction Hypotheses
• Selective inference in complex research
• Oracle and Adaptive Compound Decision Rules for False Discovery Rate Control
• Multiple Testing for Pattern Identification, With Applications to Microarray Time-Course Experiments
• Estimating the Null and the Proportion of Nonnull Effects in Large-Scale Multiple Comparisons
• Discovering Findings That Replicate From a Primary Study of High Dimension to a Follow-Up Study
• Statistical significance for genomewide studies
• Comments on: Augmenting the bootstrap to analyze high dimensional genomic data