Methods for detecting methylation by SNP interaction in GAW20 simulation

BMC Proceedings

Table 2 Proportion of tests with p < 0.05 under several models with proc GLM and proc MIXED

	Number of tests	GLM model 1a	GLM model 1b	MIXED model 1a	MIXED model 1b	MIXED model 2a	MIXED model 2b
cg0000036 * rs9661059	200	0.91	0.41	0.95	0.64	0.86	0.11
cg0004591 * rs1082841	200	0.20	0.28	0.28	0.40	0.29	0.06
cg0124267 * rs4399565	200	0.52	0.62	0.59	0.72	0.44	0.19
cg1048095 * rs736004	200	0.63	0.18	0.69	0.28	0.66	0.05
cg1877239 * rs1012116	200	0.78	0.45	0.83	0.62	0.74	0.12
Background SNPs	20,000	0.06	0.07	0.05	0.12	0.05	0.04
Null SNP interactions	453,400	0.05	0.05	0.05	0.05	0.05	0.05
Null SNP interactions (w/MAC > 50)	380,800	0.05	0.05	0.05	0.05	0.04	0.04

ISSN: 1753-6561