Estimating the proportion of true null hypotheses when the statistics are discrete

Bioinformatics
Isaac DialsinghNaomi S Altman

Abstract

In high-dimensional testing problems π0, the proportion of null hypotheses that are true is an important parameter. For discrete test statistics, the P values come from a discrete distribution with finite support and the null distribution may depend on an ancillary statistic such as a table margin that varies among the test statistics. Methods for estimating π0 developed for continuous test statistics, which depend on a uniform or identical null distribution of P values, may not perform well when applied to discrete testing problems. This article introduces a number of π0 estimators, the regression and 'T' methods that perform well with discrete test statistics and also assesses how well methods developed for or adapted from continuous tests perform with discrete tests. We demonstrate the usefulness of these estimators in the analysis of high-throughput biological RNA-seq and single-nucleotide polymorphism data. implemented in R.

References

Feb 28, 2004·Bioinformatics·Stan Pounds, Cheng Cheng
Jun 17, 2006·Bioinformatics·Stan Pounds, Cheng Cheng
Jul 11, 2008·BMC Bioinformatics·Korbinian Strimmer
Dec 17, 2009·Genome Research·Ran BlekhmanYoav Gilad
Feb 6, 2013·Biometrics·Tim BancroftDan Nettleton

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Citations

Sep 24, 2015·BMC Evolutionary Biology·Jeffrey P Vedanayagam, Daniel Garrigan
Feb 2, 2017·European Journal of Human Genetics : EJHG·Logan C WalkerAmanda B Spurdle
Aug 18, 2016·Nature Communications·Sarah KinkleyHo-Ryun Chung
May 12, 2018·Biometrical Journal. Biometrische Zeitschrift·Xiongzhi ChenJoseph F Heyse

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