PMC3677889_01
A subset with increasing power.. Values of phi (y axis, between. 4 and 1) and R (x axis, values between 1 and 4) for which power is decreasing (dark) and increasing (light). Each panel shows a combination of prevalence, k by row (.05, .3) and homozygous relative risk RRAA by column, range 2-7. Prevalences <.05 are not shown here because of similarity to the panels for k  = .05.
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 Figure 3 plots the 20th percentile of X2 statistics for two AD risk loci under various ratios of gold and silver standard cases and controls, described above in Methods.
Empirical power and asymptotic power.. Comparison of empirical power (E) to asymptotic (A) for various gammaca and R = 1 (solid line), R = 2 (dashed), R = 4 (dotted) at two loci that nominally replicate in the gold standard subset. Power is shown as 20th percentile of X2 statistics over 1000 bootstrapped replicates for empirical graphs or as 20th percentile of the chi squared distribution for asymptotic graphs, with non-centrality determined from genotypic disease model given in table 2.
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 Figure 3 plots the 20th percentile of X2 statistics for two AD risk loci under various ratios of gold and silver standard cases and controls, described above in Methods.