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 -- Sent via the guest posting facility at bioconductor.org.

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 > -- > Sent via the guest posting facility at bioconductor.org. > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor