Hello, I was hoping you could please help me understand the following errors. I'm running the following:
champ.DMR(beta=hs850kBetaMatrix,
pheno=PhenoFile$BMI_Class,
compare.group=NULL,
arraytype="EPIC",
method = "DMRcate",
minProbes=7,
adjPvalDmr=0.05,
cores=3,
## following parameters are specifically for DMRcate method.
rmSNPCH=T,
fdr=0.05,
dist=2,
mafcut=0.05,
lambda=1000,
C=2)
And the following is returned:
3 cores will be used to do parallel DMRcate computing.
<< Find DMR with DMRcate Method >>
Error in makeGenomicRatioSetFromMatrix(object, array = "IlluminaHumanMethylationEPIC", :
No rowname matches. 'rownames' need to match IlluminaHumanMethylation450k probe names.
In addition: Warning messages:
1: In logit2(beta) : NaNs produced
2: In logit2(beta) : NaNs produced
3: In if (arraytype == "450K") { :
the condition has length > 1 and only the first element will be used
4: In if (arraytype == "EPIC") { :
the condition has length > 1 and only the first element will be used
Thank you.
Hello:
The program failed at the very begining step: Mapping CpGs to annotation, thus I am a little bit suspect the problem is your beta matrix.
Could your please check if your beta matrix : hs850kBetaMatrix, contains valid CpG rownnames? Say using code: hs850kBetaMatrix[1:5,1:5] in R to check?
Best
Yuan Tian