Hi there,
I always have a bug when use ChAMP to call differential methylated regions (DMR) and I have tried many times but I still cannot get over it, hope someone could give me some help.
I used ChAMP to analyze EPIC data and after Combat, I went to the step to find differential methylation probes (DMP) and regions (DMR). DMP could be called successfully, but DMR could not. My command is that,
myDMR <- champ.DMR(beta=myCombat2,pheno=myLoad_B$pd$Sample_Group,
arraytype = "EPIC", method="Bumphunter",cores=10)
I always met the same error, its information is,
Error in nulltabs[[i]] : subscript out of bounds
Calls: champ.DMR ... bumphunter -> bumphunter -> .local -> bumphunterEngine
Execution halted
Could anyone give me some help? Really appreciate you.
Best wishes,
Yu
Hello Yu:
champ.DMR() appeared few complain before, and I did not see this error much. I suspect that it could be a problem inside bumphunter, since ChAMP imported it's function, thus it would show here. See below link:
https://github.com/rafalab/bumphunter/issues/18
You may try adjust cores of parallel in your command. Seems doParallel package is a little bit outdated.
Best
Yuan Tian
Hi Yuan,
Your suggestion is very helpful! I reduced the number of cores required from 10 to 3, and then it worked smoothly! Although 3 cores will not be enough in the future because I will run on a large number of samples then, I am still very happy now.
Thank you so much Yuan!
Best wishes,
Yu