I am having trouble creating a CNA object from a oligoSnpSet matrix after applying the crlmm package

I keep getting "genomdat must be numeric" error from my

oligoset<- OligoSetList(cnSet3, batch.name=batch(cnSet3)[1])

oligo<-oligoset[[1]]

CNA.object <- CNA(genomdat=copyNumber(oligo),chrom=chromosome(oligo), maploc=position(oligo),data.type="logratio", sampleid = sampleNames(oligo))

You haven't given enough information for anybody to help you, but there is likely enough information for you to help yourself.

Note the error says 'genomdat must be numeric', and there is a genomdat argument to CNA(). This indicates that at least some of the data you are passing in are not numeric. In addition, the help for copyNumber() says that genomdat has to be a vector or matrix. The obvious thing to do is to explore what you are passing in for the genomdat argument

genomdat <- copyNumber(oligo)

class(genomdat)

is.numeric(genomdat)

You may need to coerce the output of copyNumber() to the correct format for CNA().