Thank for developing ChAMP for methylation analysis. I was processing my methylation data for 165 samples belonging to various subgroups/ phenotypes, so I have nearly 45 contrasts created. I had a few questions:
Can I get a list of DMPs between all groups and not just specified contrasts?
Since I have a lot of contrasts, when I run champ.DMR() I also get ~300 different DMRs for each contrast, I was wondering if there is a way to filter out the most significant DMRs then? Also DMR$bumphunter gives a smaller list of DMRs, are these the DMRs between all phenotypes?
When performing GSEA using "fischer" as method, it will use all DMPs and cpg in DMRs ( which looks like it uses DMR$bumphunter) , however for all contrasts it returns same list of pathways, I would expect maybe a different list for different contrasts, no? Maybe I should also specify the DMRs separately?
I really look forward to your response and maybe a good tutorial for the huge amount of really useful information your package produces :)
Hello,
Thank for developing ChAMP for methylation analysis. I was processing my methylation data for 165 samples belonging to various subgroups/ phenotypes, so I have nearly 45 contrasts created. I had a few questions:
I really look forward to your response and maybe a good tutorial for the huge amount of really useful information your package produces :)
Many thanks in advance,
Best, Shweta