Analytic P-value calculation for the higher criticism test in finite d problems

Biometrika
Ian J Barnett, Xihong Lin

Abstract

The higher criticism is effective for testing a joint null hypothesis against a sparse alternative, e.g., for testing the effect of a gene or a genetic pathway that consists of d genetic markers. Accurate p-value calculations for the higher criticism based on the asymptotic distribution require a very large d, which is not the case for the number of genetic variants in a gene or a pathway. In this paper we propose an analytic method that accurately computes the p-value of the higher criticism test for finite d problems. Unlike previous treatments, this method does not rely on asymptotics in d or simulation, and is exact for arbitrary d when the test statistics are normally distributed. The method is particularly computationally advantageous when d is not large. We illustrate the proposed method with a case-control genome-wide association study of lung cancer and compare its power to competing methods through simulations.

References

Oct 10, 2007·American Journal of Human Genetics·Jung-Ying Tzeng, Daowen Zhang
Sep 26, 2008·Proceedings of the National Academy of Sciences of the United States of America·David Donoho, Jiashun Jin
Oct 30, 2008·Journal of the National Cancer Institute·Margaret R SpitzXifeng Wu
Jul 9, 2011·American Journal of Human Genetics·Michael C WuXihong Lin

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Citations

May 28, 2019·Journal of the American Statistical Association·Yaowu Liu, Jun Xie
Mar 28, 2020·Genetic Epidemiology·X Jessie JengJung-Ying Tzeng
Sep 12, 2018·High-throughput·Patrick BrehenyJoshua Lambert
Jul 25, 2017·Journal of the American Statistical Association·Ian BarnettXihong Lin
Dec 6, 2017·Journal of Multivariate Analysis·Sihai Dave ZhaoHongzhe Li
Aug 20, 2021·Journal of Genetics and Genomics = Yi Chuan Xue Bao·Han SunXingpeng Jiang

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