[BioC] genoset:::initGenoSet

[Pan Du]

Hi Leonard

Pete has fixed this problem in the developing version of genoset.
Thanks for reporting this!

Pan

On Wed, Feb 20, 2013 at 4:27 AM, Schalkwyk, Leonard
<leonard.schalkwyk at kcl.ac.uk> wrote:
>
>
> 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