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. 2006 Dec 22;2(12):e190. doi: 10.1371/journal.pgen.0020190

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© 2006 Patterson et al.

This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited.

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(A) We carried out 1,000 simulations of a panmictic population, where we have a sample size of m = 100 and n = 5,000 unlinked markers. We give a P–P plot of the TW statistic against the theoretical distribution; this shows the empirical cumulative distribution against the theoretical cumulative distribution for a given quantile. If the fit is good, we expect the plot will lie along the line y = x. Interest is primarily at the top right, corresponding to low p-values.

(B) P–P plot corresponding to a sample size of m = 200 and n = 50,000 markers. The fit is again excellent, demonstrating the appropriateness of the Johnstone normalization.