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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.
Consult the ChAMP.DMR documentation for more information on supported array types and expected data formats: https://bioconductor.org/packages/release/bioc/html/ChAMP. getaway shootout.html1