Table 3. Number of CpG % methylation values showing agreement within 5%, 10% and 20% ranges, between Infinium 450K and RRBS (Nreads ≥ 10) data, at different levels of Infinium processing.

Difference range (n = 387,789)	Within 20%		Within 10%		Within 5%		Spearman's rank R	Pearson's R2	Slope	MIC
Probe Type	Type I	Type II	Type I	Type II	Type I	Type II
Raw Data	166,565	192,635	147,047	145,040	114,131	69,159	0.83	0.93	0.84	0.83
	94%	92%	83%	69%	64%	33%	p < 0.001	p < 0.001
After color adjustment	166,723	195,934	148,589	148,186	119,916	67,879	0.83	0.93	0.88	0.83
	94%	93%	84%	71%	67%	32%	p < 0.001	p < 0.001
After color and Type II adjustment	166,723	199,332	148,589	172,073	119,916	130,431	0.83	0.94	0.93	0.83
	94%	95%	84%	82%	67%	62%	p < 0.001	p < 0.001
After color, Type II and QN	167,026	199,786	149,690	174,764	122,500	135,190	0.83	0.94	0.95	0.83
	94%	95%	84%	83%	69%	64%	p < 0.001	p < 0.001

The greatest number of CpGs agreeing at every level, between processing level, are bolded. Overall correlation statistics are also shown (n = 387,789).