:-D that's great news!!! benilton On 8 November 2012 11:56, Andrew Beggs <a.beggs@bham.ac.uk> wrote: > Hello**** > > ** ** > > I solved the problems. In essence, the PAIR files I had been given were > supplied without control probes in the PAIR files. Adding these locations > in with a script from the NDF file (and NA) whilst converting the PAIR > files now means it works perfectly!**** > > ** ** > > Many thanks **** > > ** ** > > Andrew**** > > ** ** > > *From:* Andrew Beggs [mailto:a.beggs@bham.ac.uk] > *Sent:* 06 November 2012 12:09 > *To:* Benilton Carvalho; Andrew Beggs > > *Cc:* P. Murakami; Andrew Jaffe; Peter Murakami; > bioconductor@r-project.org > *Subject:* RE: [BioC] CHARM - The following columns in sampleKey...**** > > ** ** > > Hi**** > > ** ** > > Yep it’s:**** > > ** ** > > seed <- new("NgsTilingPDInfoPkgSeed",ndfFile = > "2006-11-02_HG18_CpG_Promo.ndf", xysFile = "testxys2.txt",posFile = > "2006-11-02_HG18_CpG_Promo.pos", author ="Andrew Beggs", email = " > a.beggs@bham.ac.uk", biocViews = "AnnotationData",genomebuild = "HG 18", > organism = "Human", species = "Homo Sapiens", url = "")**** > > ** ** > > makePdInfoPackage(seed, destDir = ".")**** > > ** ** > > BW**** > > ** ** > > Andrew**** > > ** ** > > *From:* Benilton Carvalho [mailto:beniltoncarvalho@gmail.com] > *Sent:* 06 November 2012 12:06 > *To:* Andrew Beggs > *Cc:* P. Murakami; Andrew Jaffe; Peter Murakami; > bioconductor@r-project.org > *Subject:* Re: [BioC] CHARM - The following columns in sampleKey...**** > > ** ** > > Can you share the exact code used to create the pd package? I apologise, > but to understand what is going on, I need to recreate precisely the > scenario you describe. The package is expected to be created with 3 items: > NDF, POS and XYS files....**** > > ** ** > > ** ** > > thanks,**** > > ** ** > > b**** > > ** ** > > On 6 November 2012 11:55, Andrew Beggs <a.beggs@bham.ac.uk> wrote:**** > > Hi**** > > **** > > I get the following:**** > > **** > > > head(dbGetQuery(db(rawData),"SELECT * from featureSet"))**** > > # fsetid man_fsetid**** > > 1 6 chr10:100017797-100018797**** > > 2 7 chr10:100164731-100165731**** > > 3 8 chr10:100196494-100197494**** > > 4 9 chr10:100217275-100217975**** > > 5 10 chr10:100982061-100982762**** > > 6 11 chr10:100983644-100984344**** > > **** > > Obviously the column ID is wrong, but I used the pdInfoBuilder package to > create it as per the vignette, with the NDF unmodified. I obviously had to > convert the PAIR files from the CD to XYS files, but did this as per posts > on the bioconductor mailing lists.**** > > **** > > Thanks for all the help so far**** > > **** > > Andrew**** > > **** > > **** > > *From:* Benilton Carvalho [mailto:beniltoncarvalho@gmail.com] > *Sent:* 05 November 2012 18:09 > *To:* P. Murakami > *Cc:* Andrew Beggs; Andrew Jaffe; Peter Murakami; > bioconductor@r-project.org**** > > > *Subject:* Re: [BioC] CHARM - The following columns in sampleKey...**** > > **** > > More importantly, how was the respective pd* (annoation) package created? > Was the NDF modified in any way? If so, how?**** > > **** > > On 5 November 2012 17:56, P. Murakami <polyphemus421@gmail.com> wrote:**** > > pmChr is a function in the oligo package, not the charm package. > Apparently your dat is not a valid TilingFeatureSet object. > > If you look your error message and at the definition of pmChr--type > selectMethod(pmChr,"TilingFeatureSet")--you can see that the problem seems > to be that your dat object has no "chrom" column in its featureSet table. > To see this type > > dbGetQuery(db(dat),"SELECT * from featureSet") > > There should be a column named "chrom" with values for each probe like > "chr10", "chrX", etc. > Maybe if you study the oligo package (and maybe DBI package) more you can > figure out how to make your dat object valid. > > hth > peter > > On Mon, Nov 5, 2012 at 8:59 AM, Andrew Beggs <a.beggs@bham.ac.uk> wrote: > > > Hi**** > > > > ** ** > > > > It fails at the following line:**** > > > > ** ** > > > > chr <- pmChr(dat)**** > > > > ** ** > > > > And gives the error:**** > > > > ** ** > > > > Error in sqliteExecStatement(con, statement, bind.data) : **** > > > > RS-DBI driver: (error in statement: no such column: chrom)**** > > > > ** ** > > > > Andrew**** > > > > ** ** > > > > *From:* P. Murakami [mailto:polyphemus421@gmail.com] > > *Sent:* 02 November 2012 15:09 > > *To:* Andrew Beggs > > *Cc:* Andrew Jaffe; Peter Murakami; bioconductor@r-project.org > > > > *Subject:* Re: [BioC] CHARM - The following columns in sampleKey...**** > > > > ** ****** > > > > > Try running the code inside getControlIndex and see where it fails. > > > > Also, "The following columns in sampleKey contain discrepant values > > between channels and are being removed: 1" is not an error and is not > even > > a warning, it's just a message. The function takes a sampleKey data > frame > > with 2 rows per sample and returns one (phenoData) with 1 row per sample, > > so columns with different values in the 2 rows for the same sample can't > be > > included in that output data frame. You'll always get this message for > the > > file name column since one row has .532 and the other has .635. > > > > peter murakami > >**** > > > **** > > > > On Fri, Nov 2, 2012 at 9:54 AM, Andrew Beggs <a.beggs@bham.ac.uk> > wrote:** > > ****** > > > > > PS I have reversed the inputs, and that looks a lot better. > > > > However it still fails on point 2. > > > > I am using the BSgenome.Hsapiens.UCSC.hg18 library - do you think that > has > > anything to do with it? > > > > A > >**** > > > From: Andrew Beggs [mailto:a.beggs@bham.ac.uk]**** > > > Sent: 02 November 2012 13:42**** > > > To: Andrew Jaffe; a.beggs@bham.ac.uk; Peter Murakami; > > bioconductor@r-project.org > > Subject: RE: [BioC] CHARM - The following columns in sampleKey...******* > * > > > > > > > Hi, > > > > Thanks for your help > > > > I have solved the first part of the puzzle, it was due to incorrect > > conversion of the PAIR to XYS files. The other problems are > > > > > > 1) I get the following error when trying to do QC: > > > > > pmq= pmQuality(rawData) > > Error in tapply(x[bgIndex, i], bgNgc, ecdf) : subscript out of bounds > > > > > > 2) I thought I had this fixed, and then got this as well when I > tried > > to identify unmethylated control probes: > > > > > ctrlIdx <- getControlIndex(rawData, subject=Hsapiens, noCpGWindow=60) > > Error in sqliteExecStatement(con, statement, bind.data) : > > RS-DBI driver: (error in statement: no such column: chrom) > > > > I am using MeDIP as it happens, so I need to reverse the 532 and 635 > > inputs do you think? 532 is labelled as INPUT in the samplekey.txt and > 635 > > is MBD. > > > > Thanks > > > > Andrew > > > > > > > >**** > > > From: Andrew Jaffe [mailto:ajaffe@jhsph.edu] > > Sent: 02 November 2012 13:07**** > > > > To: a.beggs@bham.ac.uk<mailto:a.beggs@bham.ac.uk>; Peter Murakami; > > bioconductor@r-project.org<mailto:bioconductor@r-project.org>******** > > > > > Subject: Re: [BioC] CHARM - The following columns in sampleKey... > > > > Hey, > > > > What's actual code you are running? It looks like you read the data in > > with readCharm: > > > > rawData = readCharm(...) > > > > So is that discrepancy just a warning, and not an error? > > > > Also, if you are using a methyl-enrichment protocol (like MeDip) with the > > charm package, you need to reverse the inputs - charm assumes McrBC which > > enriches for unmethyled DNA, so the "treatment" input here would be the > > reverse. That might be one reason why downstream analyses are failing. > > Could you provide more code of exactly what fails later? > > > > Thanks, > > Andrew Jaffe > > > > ------------------------------ > > > > Message: 18 > > Date: Fri, 2 Nov 2012 01:25:08 -0700 (PDT) > > From: "Andrew Beggs [guest]" <guest@bioconductor.org<mailto:> > guest@bioconductor.org>>**** > > > To: bioconductor@r-project.org<mailto:bioconductor@r-project.org>, > > a.beggs@bham.ac.uk<mailto:a.beggs@bham.ac.uk>**** > > > Cc: charm Maintainer <pmurakam@jhsph.edu<mailto:pmurakam@jhsph.edu>>**** > > > Subject: [BioC] CHARM - The following columns in sampleKey... > > Message-ID: <20121102082508.CDE081429FB@mamba.fhcrc.org<mailto:> > 20121102082508.CDE081429FB@mamba.fhcrc.org>> > > > >**** > > > Hello > > > > I've being trying to get charm to read in some Nimblegen array data that > I > > had to convert from PAIR to XYS, also making an annotation file. > > > > All goes swimmingly, until I try to use readCharm, although the data > > appears to load, I get the following error when using readCharm: > > > > The following columns in sampleKey contain discrepant values between > > channels and are being removed: 1 > > > > It's not clear what this means, as I have looked at the two channel files > > (532 and 635) and the structure is essentially the same. Subsequent > > analyses fail, I assume because of missing data. > > > > If I look at my loaded dataset with rawData I get the following: > > > > > rawData > > TilingFeatureSet (storageMode: lockedEnvironment) > > assayData: 389307 features, 39 samples > > element names: channel1, channel2 > > protocolData > > rowNames: N3 N9 ... E2 (39 total) > > varLabels: filenamesChannel1 filenamesChannel2 dates1 dates2 > > varMetadata: labelDescription channel > > phenoData > > rowNames: N3 N9 ... E2 (39 total) > > varLabels: sampleID tissue arrayUT arrayMD > > varMetadata: labelDescription channel > > featureData: none > > experimentData: use 'experimentData(object)' > > Annotation: pd.2006.11.02.hg18.cpg.promo > > > > Can anyone help? > > > > -- output of sessionInfo(): > > > > R version 2.15.2 (2012-10-26) > > Platform: x86_64-pc-linux-gnu (64-bit) > > > > locale: > > [1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C > > [3] LC_TIME=en_GB.UTF-8 LC_COLLATE=en_GB.UTF-8 > > [5] LC_MONETARY=en_GB.UTF-8 LC_MESSAGES=en_GB.UTF-8 > > [7] LC_PAPER=C LC_NAME=C > > [9] LC_ADDRESS=C LC_TELEPHONE=C > > [11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C > > > > attached base packages: > > [1] stats graphics grDevices utils datasets methods base > > > > other attached packages: > > [1] pd.2006.11.02.hg18.cpg.promo_0.0.1 oligo_1.22.0 > > [3] oligoClasses_1.20.0 RSQLite_0.11.2 > > [5] DBI_0.2-5 charm_2.4.0 > > [7] genefilter_1.40.0 RColorBrewer_1.0-5 > > [9] fields_6.7 spam_0.29-2 > > [11] SQN_1.0.5 nor1mix_1.1-3 > > [13] mclust_4.0 Biobase_2.18.0 > > [15] BiocGenerics_0.4.0 > > > > loaded via a namespace (and not attached): > > [1] affxparser_1.30.0 affyio_1.26.0 annotate_1.36.0 > > [4] AnnotationDbi_1.20.2 BiocInstaller_1.8.3 Biostrings_2.26.2 > > [7] bit_1.1-9 BSgenome_1.26.1 codetools_0.2-8 > > [10] corpcor_1.6.4 ff_2.2-9 foreach_1.4.0 > > [13] GenomicRanges_1.10.3 gtools_2.7.0 IRanges_1.16.3 > > [16] iterators_1.0.6 limma_3.14.1 MASS_7.3-22 > > [19] multtest_2.14.0 parallel_2.15.2 preprocessCore_1.20.0 > > [22] siggenes_1.32.0 splines_2.15.2 stats4_2.15.2 > > [25] survival_2.36-14 sva_3.4.0 XML_3.95-0.1 > > [28] xtable_1.7-0 zlibbioc_1.4.0 > > > > -- > > Sent via the guest posting facility at bioconductor.org<**** > > > http://bioconductor.org/>. > > > > [[alternative HTML version deleted]] > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor@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@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]]