Question: methylation array group probes
0
gravatar for igor
4.6 years ago by
igor11k
United States
igor11k wrote:

Is there a good way to group probes from a methylation array (to get regions instead of single positions) and get methylation ratios for those regions?

methylation 450k • 1.1k views
ADD COMMENTlink modified 4.6 years ago by Charles Warden7.9k • written 4.6 years ago by igor11k
0
gravatar for Charles Warden
4.6 years ago by
Charles Warden7.9k
Duarte, CA
Charles Warden7.9k wrote:

I would say minfi/bumphunter is a pretty good strategy for identifying differentially methylated regions

The code may need to be updated for some programs, but you can find templates for running this type of analysis here:

https://sourceforge.net/projects/cohcap/files/Protocol_Exchange_Example.zip/download

http://www.nature.com/protocolexchange/protocols/2965#/introduction

ADD COMMENTlink written 4.6 years ago by Charles Warden7.9k

I know there are tools for differential methylation, but that's not really what I want. I don't want to group samples and find significantly different regions. I am just trying to collapse the full probe list for each sample. Regions are more meaningful than probes.

ADD REPLYlink written 4.6 years ago by igor11k

Exactly - bumphunter (in minfi), RnBeads, COHCAP, and IMA all define differentially methylated regions (in addition to sites, as an upstream step).

If you only have one sample, you can also use COHCAP to identify differentially methylated regions in that sample, but I would recommend the group analysis (with any of the 4 tools listed above) if you have multiple samples and want to looks for differences between groups.

ADD REPLYlink written 4.6 years ago by Charles Warden7.9k

I don't want differentially methylated regions which are going to change every time. I just want a constant set of regions that I can apply to any sample and then figure out later whether it's differentially methylated or not.

ADD REPLYlink written 4.6 years ago by igor11k

In relation to this question, @Charles Warden, how would you compare DMRs among 3 different conditions? I understand bumphunter output for 2 groups but I do not see the logic for 3 groups.

Thank you!

EDIT: I opened a new post describing my doubts more deeply.

ADD REPLYlink modified 19 months ago • written 19 months ago by alfonsosaera20
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