genoset:::initGenoSet
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@schalkwyk-leonard-5783
Last seen 8.1 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
methyAnalysis methyAnalysis • 927 views
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Pan Du ▴ 440
@pan-du-4636
Last seen 8.1 years ago
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
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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 >
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