Table 1. Analysis of differences in methylation between SCLC cell lines and all control cells.

	Group effect		Position effect	Cell line effect
Analysis	OR (95%CI)	P	P	σ
CpG 68	2.4 (0.8 to 7.0)	0.11	-	0.0001
CpG 69	4.5 (1.4 to 14.0)	0.010	-	0.001
CpG 68 and 69	3.3 (1.5 to 7.1)	0.003	0.58	0.0001
CpG <68	1.8 (1.1 to 3.1)	0.027	0.32	0.23
All CpGs	2.1 (1.3 to 3.4)	0.002	<0.001	0.22

A logistic regression analysis was carried out to compare methylation in the 14 SCLC cell lines (n = 48) to controls (HeLa, A549, U20S, HEK and PBMC's) (n = 21 (all 9 A549 clones included)). The group effect is displayed as an odds ratio (OR) with a 95% confidence interval (CI) for SCLC vs control, with p values <0.05 regarded as significant. It would be expected that the repeats from each cell line would be correlated. To handle this a cell-line specific random effect is included in the model. This effect is parameterised by a single standard deviation, σ. Where multiple sites are analysed the site is included as an additional covariate, as in a 2-way analysis of variance (position effect).