ChAMP.DMR error - Error in makeGenomicRatioSetFromMatrix

Question

[André]

Hi. I need to run DMRcate directly from ChAMP.DMR to replicate an analysis. When i run the function, got this error:

>     myDMRnorm7 <- champ.DMR(beta=myNorm4,
>                         pheno=myLoad$pd$Sample_Group,
>                         arraytype="EPICv1",
>                        method = "DMRcate",
>                         minProbes=7,
>                        adjPvalDmr=0.05,
>                        cores=1,
>                         rmSNPCH=F,
>                         fdr=0.001) [===========================] [<<<<< ChAMP.DMR START >>>>>]
>      ----------------------------- !!! important !!! We just upgrate champ.DMR() function, since now champ.DMP() could works on multiple
>      phenotypes, but ProbeLasso can only works on one DMP result, so if
>      your pheno parameter contains more than 2 phenotypes, and you want to
>      use ProbeLasso function, you MUST specify compare.group=c("A","B").
>      Bumphunter and DMRcate should not be influenced.
>     
>      [ Section 1:  Check Input Pheno Start ]
>     
>        You pheno is factor type.
>          Your pheno information contains following groups. >>
>          <T>:48 samples.
>          <N>:48 samples.
>     
>     [ Section 1:  Check Input Pheno Done ]
>     
>     
>      [ Section 2:  Run DMR Algorithm Start ]
>     
>      1 cores will be used to do parallel DMRcate computing. << Find DMR with DMRcate Method >> Error in makeGenomicRatioSetFromMatrix(mat
> = object, array = "IlluminaHumanMethylationEPICv2",  :    No rownamematches. 'rownames' need to match IlluminaHumanMethylation450k
> probe names.

The same error happens when arraytype="EPIC"

The rownames look normal rownames(myNorm4) [1] "cg07881041" "cg03513874" "cg05451842" "cg14797042" "cg09838562" "cg25458538" "cg09261072" [8] "cg02404579" "cg04118974" "cg01236347" "cg22585117" "cg25552317" "cg23875663" "cg07659892"

ChAMP version: 2.34.0 ChAMPdata version: 2.36.0 DMRcate version: 3.0.1.0

Thanks for any help.