Thanks, I should have checked the devel version myself. leo On 20 Feb 2013, at 17:27, Pan Du wrote: > 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 >