dmr analysis

[lawrence ong]

Hi, 

Is there any way to account for multiple testing using the diffmeth/hmr/dmr pipeline? The dmr output gives only the region, total CpG context C's and differentially methylated C's in the region without any p values. 

The user guide also suggests that there may be differentially methylated C's which do not show up in dmr output because they do not lie within an hmr? Is this correct?

For the above reasons, I was wondering whether it would be better to run the radmeth pipeline to compare 2 groups of < 3 methylomes e.g. 1v1 or 2v2? 

Thank you

Lawrence 

[Andrew D. Smith]

I advise doing both. But yes, you should definitely try radmeth for this situation. Let me know how it works.