[BioC] Problem running HumMeth27QCReport after upgrading R to 2.15

Martin Morgan mtmorgan at fhcrc.org
Thu May 24 15:05:03 CEST 2012


On 05/23/2012 12:52 PM, Niles Oien wrote:
> Thanks! It looks like that's what is going on - the R upgrade caused a
> reinstall of the Bioconductor stuff, so the behavior changed.
>
> Rather than add column names, I went into the HumMeth27QCReport source and
> specified what separator to use. Obviously that only works for my data.
>
> I will see if I can add a function to HumMeth27QCReport that detects the
> separator in a text file, and then use that separator when methylumi reads
> the methylation data. I think that would make things more robust as it
> would reduce HumMeth27QCReport's dependance on the Bioconductor behavior.

For what it's worth HumMeth27QCReport is not a Bioconductor package; 
might as well include the maintainer

   packageDescription("HumMeth27QCReport")$Maintainer

in the thread.

Martin

>
> Thanks again,
>
> Niles.
>
>
> On Wed, May 23, 2012 at 12:31 PM, Djie Tjwan Thung<djie.thung at gmail.com>wrote:
>
>> Hi Niles,
>>
>> I stumbled upon somewhat the same problem as you, although I do not use
>> HumMeth27QCReport. Since Bioconductor 2.10, methylumi reads methylation
>> files differently:
>>
>> For a methylation file it tries to guess what seperator delimits your file
>> by calling the function inside methylumiR:
>>
>> .getFileSeparator(filename)
>>
>> the function .getFileSeperator then tries to automatically detect which
>> seperator delimits the file by assuming your file has at least one column
>> with ProbeID in its name:
>>   ## Use "ProbeID" as an indicator of Where the metaData stops
>> ##   intelligently find nMetaDataLines
>>   nMetaDataLines<- grep('ProbeID', info, ignore.case=TRUE) - 1
>>
>> The methylation demo data of HumMeth27QCReport lacks a ProbeID column and
>> I assume you also miss such a column in your methylation data. As several
>> functions of HumMeth27QCReport, act as wrapper functions around lumi and
>> methylumi functions, I guess this is why the problem occurs.
>>
>> If you can export your methylation files again with ProbeID columns (I
>> believe they are called ProbeID_A and ProbeID_B), try this and run
>> HumMeth27QCReport once again. I think this will fix your problem.
>>
>> Regards,
>> Djie Thung
>>
>> 2012/5/23 Niles Oien [guest]<guest at bioconductor.org>
>>
>>>
>>>
>>> Hi,
>>>
>>> I just upgraded R from 2.14 to 2.15 and I am finding that the
>>> HumMeth27QCReport package no longer runs, even on the demo data that come
>>> with the package.
>>>
>>> What I do is :
>>>
>>> library(HumMeth27QCReport)
>>> Dir<- "/my/dir/Methylation/demo27"
>>> Plat<- "Hum27"
>>> ImportDataR<- ImportData(Dir)
>>> ControlResults<- getAssayControls(ImportDataR,
>>>                                    platform=Plat)
>>>
>>> QCResults<- QCCheck(ImportDataR, pval=0.05)
>>>
>>> normMvalues<- HumMeth27QCReport(ImportDataR,
>>>          platform=Plat, pval=0.05, ChrX=FALSE, "euclidian")
>>>
>>> but for the calls to QCCheck() and HumMeth27QCReport() I get the message :
>>>
>>> Error in gregexpr(sep.i, dataLine1)[[1]] : subscript out of bounds
>>>
>>> Any suggestions would be appreciated, I am appending my sessionInfo()
>>> from R.
>>>
>>> Thanks,
>>>
>>> Niles Oien, University of Colorado, Boulder, USA.
>>>
>>>
>>>
>>>> sessionInfo()
>>> R version 2.15.0 (2012-03-30)
>>> Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
>>>
>>> locale:
>>> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
>>>
>>> attached base packages:
>>>   [1] tcltk     grid      splines   stats     graphics  grDevices utils
>>>    datasets  methods   base
>>>
>>> other attached packages:
>>>   [1] BiocInstaller_1.4.4                   HumMeth27QCReport_1.2.14
>>>         tcltk2_1.2-3
>>>   [4] WriteXLS_2.1.0                        plotrix_3.4-1
>>>          gplots_2.10.1
>>>   [7] KernSmooth_2.23-7                     caTools_1.12
>>>         bitops_1.0-4.1
>>> [10] gdata_2.8.2                           gtools_2.6.2
>>>         Hmisc_3.9-3
>>> [13] survival_2.36-14                      amap_0.8-7
>>>         IlluminaHumanMethylation450k.db_1.4.6
>>> [16] IlluminaHumanMethylation27k.db_1.4.6  org.Hs.eg.db_2.7.1
>>>         RSQLite_0.11.1
>>> [19] DBI_0.2-5                             AnnotationDbi_1.18.0
>>>         lumi_2.8.0
>>> [22] nleqslv_1.9.3                         methylumi_2.2.0
>>>          ggplot2_0.9.1
>>> [25] reshape2_1.2.1                        scales_0.2.1
>>>         Biobase_2.16.0
>>> [28] BiocGenerics_0.2.0
>>>
>>> loaded via a namespace (and not attached):
>>>   [1] affy_1.34.0           affyio_1.24.0         annotate_1.34.0
>>> bigmemory_4.2.11      Biostrings_2.24.1     BSgenome_1.24.0
>>>   [7] cluster_1.14.2        colorspace_1.1-1      dichromat_1.2-4
>>> digest_0.5.2          DNAcopy_1.30.0        GenomicRanges_1.8.6
>>> [13] genoset_1.6.0         hdrcde_2.16           IRanges_1.14.3
>>>   labeling_0.1          lattice_0.20-6        MASS_7.3-18
>>> [19] Matrix_1.0-6          memoise_0.1           mgcv_1.7-16
>>> munsell_0.3           nlme_3.1-103          plyr_1.7.1
>>> [25] preprocessCore_1.18.0 proto_0.3-9.2         RColorBrewer_1.0-5
>>>   RCurl_1.91-1          Rsamtools_1.8.4       rtracklayer_1.16.1
>>> [31] stats4_2.15.0         stringr_0.6           tools_2.15.0
>>>   XML_3.9-4             xtable_1.7-0          zlibbioc_1.2.0
>>>
>>>
>>>
>>>   -- output of sessionInfo():
>>>
>>>
>>> Error in gregexpr(sep.i, dataLine1)[[1]] : subscript out of bounds
>>>
>>> --
>>> Sent via the guest posting facility at bioconductor.org.
>>>
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>>
>>
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