Question: genoset:::initGenoSet
0
gravatar for Schalkwyk, Leonard
6.5 years ago by
Schalkwyk, Leonard20 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
methyanalysis • 577 views
ADD COMMENTlink modified 6.5 years ago by Pan Du440 • written 6.5 years ago by Schalkwyk, Leonard20
Answer: genoset:::initGenoSet
0
gravatar for Pan Du
6.5 years ago by
Pan Du440
Pan Du440 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
ADD COMMENTlink written 6.5 years ago by Pan Du440
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 >
ADD REPLYlink written 6.5 years ago by Schalkwyk, Leonard20
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 258 users visited in the last hour