Critical values and variation in type I error along chromosomes in the COGA dataset using the applied pseudo-trait method

Table 3 5th percentile of whole genome p-value distribution, by type of pseudo-trait (Affymetrix data)

	All pseudo-traits	Allele-count pseudo-traits	Normal + allele-count pseudo-traits	Uniform	Normal
# pseudo-traits	80	39	39	1	1
Haseman-Elston
mean	0.010	0.011	0.007	0	0
SD	0.039	0.036	0.043	0.040	0.046
ROMP-one
mean	0.009	0.008	0.010	0	0
SD	0.048	0.049	0.047	0.059	0.039
ROMP/ROOP-one
mean	0.043	0.044	0.041	0.059	0.039
SD	0.011	0.011	0.012	0	0
ROMP-all
mean	0.015	0.009	0.012	0	0
SD	0.038	0.049	0.028	0.042	0.029
ROMP/ROOP-all
mean	0.013	0.012	0.013	0	0
SD	0.026	0.029	0.023	0.042	0.029

ISSN: 2730-6844