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Genetics, Vol. 178, 609-610, January 2008, Copyright © 2008
doi:10.1534/genetics.107.074609

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Naive Application of Permutation Testing Leads to Inflated Type I Error Rates

G. A. Churchill* and R. W. Doerge{dagger},1

* The Jackson Laboratory, Bar Harbor, Maine 04609 and {dagger} Department of Statistics, Purdue University, West Lafayette, Indiana 47907

1 Corresponding author: 150 N. University St., Purdue University, W. Lafayette, IN 47907.
E-mail: doerge{at}purdue.edu

Failure to account for family structure within populations or in complex mating designs via uninformed applications of permutation testing will lead to inflated type I error rates. Careful consideration of the design factors is essential since some situations allow several valid permutation strategies, and the choice that maximizes statistical power will not always be intuitive.


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