Beta matrix
There exists a transformation between M value (analyzed here, and first introduced in this paper) and the Beta value (formula for transformation is also described here):
beta=2^M/(2^M+1); M=log2(M/U); beta=M/(M+U+offset)
Data distribution based on the expression used for measuring DNA methylation (beta vs M value):
I used the matrix of M values and transformed them into beta values. Here are the plots of the first eigengene, first eigenarray (colored by the probe dye) and the outliers identified in the first eigengene:
Density plots by the color of the dye of the first 3 eigenarrays: 
Consultation with Brig and Justin: don't split the data, keep all probes together.