Table 2.

Summary of Intraclass correlation coefficients of CpG locus methylation, for non-sex and sex chromosomes, in Beta and M scale.

Non-Sex Chromosome
			Median ICCs (Beta Values)			Median ICCs (M Values)
		N	Model 1*	Model 2**	Model 3***	Model 1*	Model 2**	Model 3***
ComBat	All	7,76,725	0.22	0.19	0.20	0.22	0.19	0.19
	Enhancer	1,21,164	0.31	0.27	0.28	0.30	0.27	0.27
	Known DMR	36,358	0.37	0.32	0.32	0.36	0.31	0.31
	Infinium I	1,23,815	0.13	0.11	0.11	0.13	0.11	0.11
	Infinium II	6,52,910	0.24	0.21	0.22	0.24	0.21	0.21
Non ComBat	All	7,76,725	0.50	0.45	0.45	0.49	0.44	0.44
	Enhancer	1,21,164	0.55	0.51	0.50	0.54	0.50	0.49
	Known DMR	36,358	0.66	0.62	0.61	0.64	0.59	0.59
	Infinium I	1,23,815	0.49	0.45	0.44	0.50	0.45	0.44
	Infinium II	6,52,910	0.50	0.45	0.45	0.49	0.44	0.44
Sex Chromosome
			Median ICCs (Beta Values)			Median ICCs (M Values)
		N	Model 1*	Model 2**	Model 3***	Model 1*	Model 2**	Model 3***
ComBat	All	17,545	0.71	0.72	0.72	0.70	0.71	0.71
	Enhancer	1,058	0.75	0.76	0.77	0.74	0.76	0.76
	Known DMR	1,155	0.77	0.78	0.78	0.77	0.78	0.78
	Infinium I	2,988	0.69	0.69	0.70	0.68	0.69	0.69
	Infinium II	14,557	0.72	0.73	0.73	0.71	0.72	0.72
Non ComBat	All	17,545	0.85	0.85	0.85	0.84	0.84	0.84
	Enhancer	1,058	0.87	0.87	0.87	0.86	0.86	0.86
	Known DMR	1,155	0.88	0.88	0.88	0.88	0.88	0.88
	Infinium I	2,988	0.83	0.83	0.83	0.83	0.83	0.82
	Infinium II	14,557	0.85	0.86	0.86	0.84	0.84	0.84

ICC: Intraclass correlation coefficient, DMR: differentially methylated regions

* Crude model, ** Crude model adjusted for cell type, ***Crude model adjusted for cell type and age