Null-free False Discovery Rate Control Using Decoy Permutations

doi:10.1007/s10255-022-1077-5

	Null-free False Discovery Rate Control Using Decoy Permutations
	He, Kun 1,3; Li, Meng-jie 2,3; Fu, Yan 2,3; Gong, Fu-zhou 2,3; Sun, Xiao-ming 1,3
	2022-04-01
发表期刊	ACTA MATHEMATICAE APPLICATAE SINICA-ENGLISH SERIES
ISSN	0168-9673
卷号	38 期号:2 页码:235-253
摘要	The traditional approaches to false discovery rate (FDR) control in multiple hypothesis testing are usually based on the null distribution of a test statistic. However, all types of null distributions, including the theoretical, permutation-based and empirical ones, have some inherent drawbacks. For example, the theoretical null might fail because of improper assumptions on the sample distribution. Here, we propose a null distribution-free approach to FDR control for multiple hypothesis testing in the case-control study. This approach, named target-decoy procedure, simply builds on the ordering of tests by some statistic or score, the null distribution of which is not required to be known. Competitive decoy tests are constructed from permutations of original samples and are used to estimate the false target discoveries. We prove that this approach controls the FDR when the score function is symmetric and the scores are independent between different tests. Simulation demonstrates that it is more stable and powerful than two popular traditional approaches, even in the existence of dependency. Evaluation is also made on two real datasets, including an arabidopsis genomics dataset and a COVID-19 proteomics dataset.
关键词	multiple testing false discovery rate null distribution-free p-value-free decoy permutations knockoff filter
DOI	10.1007/s10255-022-1077-5
收录类别	SCI
语种	英语
资助项目	National Key R&D Program of China[2018YFB0704304] ; National Natural Science Foundation of China[32070668] ; National Natural Science Foundation of China[62002231] ; National Natural Science Foundation of China[61832003] ; National Natural Science Foundation of China[61433014] ; K.C. Wong Education Foundation
WOS研究方向	Mathematics
WOS类目	Mathematics, Applied
WOS记录号	WOS:000781349200001
出版者	SPRINGER HEIDELBERG
引用统计	被引频次：5[WOS] [WOS记录] [WOS相关记录]
文献类型	期刊论文
条目标识符	http://119.78.100.204/handle/2XEOYT63/18903
专题	中国科学院计算技术研究所期刊论文_英文
通讯作者	Fu, Yan
作者单位	1.Chinese Acad Sci, Inst Comp Technol, Beijing 100190, Peoples R China 2.Chinese Acad Sci, Acad Math & Syst Sci, RCSDS, CEMS,NCMIS, Beijing 100190, Peoples R China 3.Univ Chinese Acad Sci, Beijing 100049, Peoples R China
推荐引用方式 GB/T 7714	He, Kun,Li, Meng-jie,Fu, Yan,et al. Null-free False Discovery Rate Control Using Decoy Permutations[J]. ACTA MATHEMATICAE APPLICATAE SINICA-ENGLISH SERIES,2022,38(2):235-253.
APA	He, Kun,Li, Meng-jie,Fu, Yan,Gong, Fu-zhou,&Sun, Xiao-ming.(2022).Null-free False Discovery Rate Control Using Decoy Permutations.ACTA MATHEMATICAE APPLICATAE SINICA-ENGLISH SERIES,38(2),235-253.
MLA	He, Kun,et al."Null-free False Discovery Rate Control Using Decoy Permutations".ACTA MATHEMATICAE APPLICATAE SINICA-ENGLISH SERIES 38.2(2022):235-253.