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Naive application of permutation testing leads to inflated type I error rates

Churchill GA, Doerge RW.
The Jackson Laboratory, Bar Harbor, Maine 04609, USA.

Abstract:
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. [1]

  1. Churchill GA & Doerge RW (2008) Naive application of permutation testing leads to inflated type I error rates. Genetics 178: 609-10 PubMed
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