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.

Thanks again,

Niles.


On Wed, May 23, 2012 at 12:31 PM, Djie Tjwan Thung <djie.thung@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@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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