ChAMP.DMR error - Error in makeGenomicRatioSetFromMatrix
0
0
Entering edit mode
AndrĂ© • 0
@d92a5d17
Last seen 7 days ago
Brazil

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.

ChAMP • 75 views
ADD COMMENT
0
Entering edit mode

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

ADD REPLY

Login before adding your answer.

Traffic: 465 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6