[BioC] genoset:::initGenoSet

[Schalkwyk, Leonard]

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