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. >>> >>> _______________________________________________ >>> 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 >>> >> >> > > [[alternative HTML version deleted]] > > _______________________________________________ > 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 -- Computational Biology Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. 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