Open Access
June 2010 A geometric interpretation of the permutation p-value and its application in eQTL studies
Wei Sun, Fred A. Wright
Ann. Appl. Stat. 4(2): 1014-1033 (June 2010). DOI: 10.1214/09-AOAS298


Permutation p-values have been widely used to assess the significance of linkage or association in genetic studies. However, the application in large-scale studies is hindered by a heavy computational burden. We propose a geometric interpretation of permutation p-values, and based on this geometric interpretation, we develop an efficient permutation p-value estimation method in the context of regression with binary predictors. An application to a study of gene expression quantitative trait loci (eQTL) shows that our method provides reliable estimates of permutation p-values while requiring less than 5% of the computational time compared with direct permutations. In fact, our method takes a constant time to estimate permutation p-values, no matter how small the p-value. Our method enables a study of the relationship between nominal p-values and permutation p-values in a wide range, and provides a geometric perspective on the effective number of independent tests.


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Wei Sun. Fred A. Wright. "A geometric interpretation of the permutation p-value and its application in eQTL studies." Ann. Appl. Stat. 4 (2) 1014 - 1033, June 2010.


Published: June 2010
First available in Project Euclid: 3 August 2010

zbMATH: 1194.62121
MathSciNet: MR2758431
Digital Object Identifier: 10.1214/09-AOAS298

Keywords: effective number of independent tests , gene expression quantitative trait loci (eQTL) , Permutation p-value

Rights: Copyright © 2010 Institute of Mathematical Statistics

Vol.4 • No. 2 • June 2010
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