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Schalkwyk, Leonard
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@schalkwyk-leonard-5783
Last seen 10.2 years ago
When generating a MethyGenoSet to try out the methyAnalysis package, I
got the following:
> c <- MethyLumiM2GenoSet(b)
Error in genoset:::initGenoSet(type = "MethyGenoSet", locData
= locData, :
Mismatch between sampleNames and rownames of pData
>
> all.equal(sampleNames(b), rownames(pData(b)))
[1] TRUE
it turns out to be because of the following lines in
genoset:::initGenoSet
rownames(pData) = make.names(rownames(pData), unique = TRUE)
if (!setequal(rownames(pData), sampleNames(ad))) {
stop("Mismatch between sampleNames and rownames of pData")
}
which guarantees that a confusing 'Mismatch' will be reported if the
sampleNames start with
[0-9]. In the case of Illumina DNA methylation arrays this is true
of the default names.
Can I suggest that make.names() is run on both sampleNames and
rownames (or,
preferably, on neither) before this test is run?
Leo Schalkwyk