Question: Determine "global" methylation from Illumina EPIC data?
gravatar for Ellen O
11 months ago by
Ellen O10
Stellenbosch University
Ellen O10 wrote:

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!

methylation infinium epic • 408 views
ADD COMMENTlink modified 11 months ago by andrew.j.skelton735.3k • written 11 months ago by Ellen O10
gravatar for andrew.j.skelton73
11 months ago by
andrew.j.skelton735.3k wrote:

Take a look at the ShinyMethyl package which will help you pick out these sample level issues.

ADD COMMENTlink written 11 months ago by andrew.j.skelton735.3k
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1241 users visited in the last hour