Question: Assessing DMRs between treatment groups: subtracting control group DMRs to account for "baseline" methylation
gravatar for Ellen O
3.9 years ago by
Ellen O10
Stellenbosch University
Ellen O10 wrote:

I am currently awaiting Illumina methylationEPIC (850k) data and in the mean time figuring out how to assess DMRs with demo data. I am new to these analyses but I am making use of the Maksimovic et al. cross-package workflow (, which I have found very useful thus far.

I have three sample groups: healthy controls, poor treatment responders, and good treatment responders. I was wondering if it is possible to "subtract" the differential methylation seen within the controls before comparing the two treatment groups, so that I can account for a baseline/ "normal" level of variable methylation. Would this be possible in limma, minfi or any other packages? Or would it make more sense to just compare all three groups to each other?

Thanks in advance for any assistance!

methylationepic dmr 850k illumina • 1.1k views
ADD COMMENTlink modified 3.6 years ago by hongbo91920 • written 3.9 years ago by Ellen O10
gravatar for andrew.j.skelton73
3.9 years ago by
andrew.j.skelton736.1k wrote:

Others may be able to correct me if I'm wrong... but if you're making a contrast matrix in Limma, you could just do something along the lines of:

(healthy_control - poor_response) - (healthy_control - good_response)
ADD COMMENTlink written 3.9 years ago by andrew.j.skelton736.1k

Thanks Andrew, I will try it out!

ADD REPLYlink written 3.9 years ago by Ellen O10
gravatar for hongbo919
3.6 years ago by
hongbo91920 wrote:

I suggest using the DMR identification software based on entropy such QDMR (for pre-defined regions) or SMART (for de novo identification of DMRs from BS-Seq data). As there are multiple samples in the same group, the DMC function of SMART should work for your project.

ADD COMMENTlink written 3.6 years ago by hongbo91920
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: 1676 users visited in the last hour