I have Illumina MethylationEPIC data for a group of samples. From looking at M- and B- value distributions, It seems a few of the samples display consistently different methylation levels across the genome (in other words it's not probe-specific).
Is it possible to determine "global"/ total methylation for each sample from the genome-wide data, and how would I do this? In other words, I'd like to see if these specific samples display overall hypo- or hyper-methylation. Could this be as simple as looking at the average M-value for all the probes for each sample?
I have been working in R with minfi and limma.
Apologies if this is a stupid question, I am very new to these analyses!