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
Could anyone give me some help? Really appreciate you.