Question: Help with Errors in DMRcate ChAMP package
0
gravatar for urvi
15 months ago by
urvi0
urvi0 wrote:

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.

 

champ • 245 views
ADD COMMENTlink written 15 months ago by urvi0

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

ADD REPLYlink written 15 months ago by Yuan Tian120
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