[BioC] IMA Peak Correction Error - subscript out of bounds

[Dan Tenenbaum]

Hi Scott,

On Mon, Jan 7, 2013 at 7:49 AM, Scott Robinson [guest]
<guest at bioconductor.org> wrote:
>
> I am running the IMA pipeline script on data gathered using the 450K Illumina methylation chip. It works fine except if I choose to do peak correction in which case I get the error:
>
> "Error in peak.correction(bmatrix, annotation) : subscript out of bounds"
>
> Does anyone know why I might be getting this error? I have not changed any parameters besides the peak correction boolean and it works fine without doing the peak correction.
>
> The two commands and their responses follow:
>
>> data =IMA.methy450R(fileName = MethyFileName,columnGrepPattern=list(beta=".AVG_Beta",detectp=".Detection Pval"),groupfile = PhenoFileName) ## load the data
> For a desktop with 2GB memory and 7200RPM hard disk,
> the estimated time of this process is 1-2 mins for a dataeset with 10 samples and 6-7 mins for a dataset with 200 samples
> ......Extracting the beta value matrix.....
> ......Extracting the pvalue matrix......
> ......Extracting the annotation matrix......
> Read phenotype data...
> Matching the orders of samples between phenotype data and beta value matrix.
> Total CpG sites without any filtering are: 485577
> Total samples are: 24
> ....Starting Quality Control...
> An exprmethy450 class are created and the slotNames are:
>  bmatrix annot detectP groupinfo
> Basic Quality Control information can be found in QC.pdf file
>>
>> dataf = IMA.methy450PP(data,na.omit = na.omit,normalization=normalization,peakcorrection = peakcorrection,transfm = transfm,samplefilterdetectP = samplefilterdetectP,samplefilterperc = samplefilterperc,sitefilterdetectP = sitefilterdetectP,locidiff = locidiff, locidiffgroup = locidiffgroup,XYchrom = XYchrom,snpfilter = snpfilter) ## QC filtering
> 0 samples removed with at least 75 percentage sites having pvalue greater than 1e-05
> 6052 sites contain missing value and are removed
> 101 sites had at least 75 % samples with pvalue great than 0.05 and are removed
> 479424 sites were retained from the original 485577 sites
> Peak correction...
> This part of code was provided by Matthieu Defrance <defrance at bigre.ulb.ac.be>
> Thanks for sharing the code with us.
> Dimension of beta matrix 479424 12
> Dimension of annotation 479424 15
> Error in peak.correction(bmatrix, annotation) : subscript out of bounds
>
>  -- output of sessionInfo():
>
> R version 2.15.2 (2012-10-26)
> Platform: x86_64-w64-mingw32/x64 (64-bit)
>
> locale:
> [1] LC_COLLATE=English_United Kingdom.1252  LC_CTYPE=English_United Kingdom.1252
> [3] LC_MONETARY=English_United Kingdom.1252 LC_NUMERIC=C
> [5] LC_TIME=English_United Kingdom.1252
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
>  [1] IMA_3.1.2             dplR_1.5.6            preprocessCore_1.20.0
>  [4] bioDist_1.30.0        KernSmooth_2.23-8     Biobase_2.18.0
>  [7] BiocGenerics_0.4.0    MASS_7.3-22           limma_3.14.3
> [10] WriteXLS_2.3.0
>
> loaded via a namespace (and not attached):
> [1] digest_0.6.0    grid_2.15.2     lattice_0.20-10 stringr_0.6.2   XML_3.95-0.1
>
>

IMA is not a Bioconductor package so you might ask its maintainer
whose contact info is here:

http://www.rforge.net/IMA/

Dan


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