Question: Determine "global" methylation from Illumina EPIC data?
gravatar for Ellen O
9 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 • 353 views
ADD COMMENTlink modified 9 months ago by andrew.j.skelton735.1k • written 9 months ago by Ellen O10
gravatar for andrew.j.skelton73
9 months ago by
andrew.j.skelton735.1k wrote:

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

ADD COMMENTlink written 9 months ago by andrew.j.skelton735.1k
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: 1574 users visited in the last hour