Networks dissimilarity measure as it is defined here.

Beta vs M value (-batch, center, plate column and row (BCRC))	0.32
Beta vs M value (-batch, plate column and row (CENTER))	0.27
M value (BCRC) vs M value (CENTER)	0.12

Beta (vertical) vs M value (-batch, center, plate column and row (BCRC)) (horizontal):

Beta vs M value (CENTER):

M value (BCRC) vs M value (Center):

Summary of network modules correlations with clinical traits:

traits	Beta	M value (BCRC)	M value (BCR)	mb	mbc
% variance explained	60-73%	45-80%	45-80%	15-60%	15-66%
number of modules	8	18	8	65	79
survival (P value=0.05)	0	0	0 (red=0.0509)	6	8
primary therapy outcome	0	0	1 (red)
age	1	6	1
tumor grade	1	1	0
tumor stage	0	0	0
Tumor residual disease	0	1	1
Chromosomal clustering	2	4	1 (brown)	27	52
Gene Ontology	keratinization	keratinization	keratinization	weak	weak

November 16th, 2011 update: We decided to choose M value as a measure for methylation and normalization -batch, -center, -plate row, -plate column for all further analyses.

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