[BioC] importing data problem with methyAnalysis package

[Pan Du]

Hi Xuan

Thanks for reporting this. The reason of this error is that your
sampleNames start with a numeric number. The genoset:::initGenoSet
function forces the pData rownames to be syntax valid, which makes it
inconsistent with its sampleNames. I will report this to Peter
(genoset package author). As a temporary solution, you can manually
change the sampleNames:
  sampleNames(dataM) <- make.names(sampleNames(dataM))

For your second annotation question, the nuID annotation packages were
designed for the Illumina expression arrays. For DNA methylation
arrays, you can directly use 'IlluminaHumanMethylation450k.db', no
need to do any id conversion. The methyAnalysis package also has an
"annotateGRanges" function for annotating your interested CpG-sites or
methylation region.

Pan

On Sun, Jan 6, 2013 at 6:58 AM, 王玄 <wangxuan at moon.ibp.ac.cn> wrote:
> Hello Pan Du,
>
>          Recently I am working with some data generated by Illumina 450k.
> Your “lumi” package is an excellent package. With its help I did some
> preprocessing. Then I chose your “methyAnalysis” package because it’s
> designed to work with “lumi”, this would be very convenient. But I failed at
> the beginning.
>
>          I tried to search the solution, but got nothing. Could I borrow a
> minute of your time helping me deal with this issue?
>
>
>
> My commands are shown below:
>
>
>
>> dataM<-lumiMethyR('head.txt',lib='IlluminaHumanMethylation450k.db')
>
>> methyGenoSet <- MethyLumiM2GenoSet(dataM)
>
> Error on genoset:::initGenoSet(type = "MethyGenoSet", locData = locData,  :
>
>   Mismatch between sampleNames and rownames of pData
>
>> pData(dataM)
>
>                            sampleID             label
>
> 5911874030_R01C01 5911874030_R01C01 5911874030_R01C01
>
> 5911874030_R02C01 5911874030_R02C01 5911874030_R02C01
>
> 5911874030_R03C01 5911874030_R03C01 5911874030_R03C01
>
> 5911874030_R04C01 5911874030_R04C01 5911874030_R04C01
>
> 5911874030_R05C01 5911874030_R05C01 5911874030_R05C01
>
>
>
> I will attach some of my data ( used by example code shown above ) to you.
>
> My working environment is shown below:
>
> Windows 7 Ultimate OEM x64
>
> R 2.15.2 x64
>
> Bioconductor 2.11
>
> lumi 2.10.0
>
> methyAnalysis 1.0.0
>
>
>
> By the way, I was also confused with how to annotate gene with “lumi”
> package. According to “IlluminaAnnotation.pdf” in “lumi”, I should generate
> nuID first. But Illumina 450k has two kinds of assay, the assay II would
> contains not only ATCG but also R. So I can’t get the nuID of each probe.
> Then what is the recommended way to annotate with “lumi”?
>
>
>
> Would you kindly answer my questions? Many thanks!
>
>
>
>
>
>
> Wang Xuan
>
>
>
> Key Laboratory of Protein and Peptide Pharmaceuticals,
>
> Institute of Biophysics, CAS.
>
> 15 Datun Road, Chaoyang District
>
> Beijing, 100101
>
> P.R.China
>
>
>
>
>
>