Multiple testing with discrete data: proportion of true null hypotheses and two adaptive FDR procedures

DOI10.1002/BIMJ.201700157zbMATH Open1400.62253arXiv1410.4274OpenAlexW2753529075WikidataQ88635324 ScholiaQ88635324MaRDI QIDQ4584975FDOQ4584975

Authors: Xiongzhi Chen, Rebecca W. Doerge, Joseph F. Heyse 

Publication date: 5 September 2018

Published in: Biometrical Journal (Search for Journal in Brave)

Abstract: We consider multiple testing with false discovery rate (FDR) control when p-values have discrete and heterogeneous null distributions. We propose a new estimator of the proportion of true null hypotheses and demonstrate that it is less upwardly biased than Storey's estimator and two other estimators. The new estimator induces two adaptive procedures, i.e., an adaptive Benjamini-Hochberg (BH) procedure and an adaptive Benjamini-Hochberg-Heyse (BHH) procedure. We prove that the the adaptive BH procedure is conservative non-asymptotically. Through simulation studies, we show that these procedures are usually more powerful than their non-adaptive counterparts and that the adaptive BHH procedure is usually more powerful than the adaptive BH procedure and a procedure based on randomized p-value. The adaptive procedures are applied to a study of HIV vaccine efficacy, where they identify more differentially polymorphic positions than the BH procedure at the same FDR level.

Full work available at URL: https://arxiv.org/abs/1410.4274

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zbMATH Keywords

false discovery ratemultiple testingheterogeneous null distributionsmultiple hypotheses testingproportion of true null hypothesesdiscrete \(p\) values

Mathematics Subject Classification ID

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

Cited In (16)

• Multiple-testing procedures based on generalized inference of true null hypotheses proportion
• False discovery rate control for multiple testing based on discrete \(p\)-values
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• Empirical Bayes cumulative \(\ell\)-value multiple testing procedure for sparse sequences
• Comments on Dr. Aniket Biswas' Letter to the Editor
• On Benjamini-Hochberg procedure applied to mid \(p\)-values
• Adaptive false discovery rate control under independence and dependence
• Estimating the proportion of true null hypotheses and adaptive false discovery rate control in discrete paradigm
• Multiple testing of composite null hypotheses for discrete data using randomized \(p\)-values
• New FDR bounds for discrete and heterogeneous tests
• Online multiple testing with super-uniformity reward
• New results for adaptive false discovery rate control with \(p\)-value weighting
• Controlling the false discovery exceedance for heterogeneous tests
• False discovery rate envelopes
• A Modified False Discovery Rate Multiple-Comparisons Procedure for Discrete Data, Applied to Human Immunodeficiency Virus Genetics

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