Question: CHARM - The following columns in sampleKey...
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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.
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ADD COMMENTlink modified 7.0 years ago by Andrew Jaffe120 • written 7.0 years ago by Guest User12k
Answer: CHARM - The following columns in sampleKey...
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7.0 years ago by
Andrew Jaffe120
Andrew Jaffe120 wrote:
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> To: bioconductor@r-project.org, a.beggs@bham.ac.uk Cc: charm Maintainer <pmurakam@jhsph.edu> Subject: [BioC] CHARM - The following columns in sampleKey... Message-ID: <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. [[alternative HTML version deleted]]
ADD COMMENTlink written 7.0 years ago by Andrew Jaffe120
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; Peter Murakami; 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:2012110 2082508.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]]
ADD REPLYlink written 7.0 years ago by Andrew Beggs90
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:2012110 2082508.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]]
ADD REPLYlink written 7.0 years ago by Andrew Beggs90
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]]
ADD REPLYlink written 7.0 years ago by P. Murakami30
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<mailto: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<mailto:a.beggs@bham.ac.uk>] Sent: 02 November 2012 13:42 To: Andrew Jaffe; 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... 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<mailto:ajaffe@jhsph.edu>] Sent: 02 November 2012 13:07 To: a.beggs@bham.ac.uk<mailto:a.beggs@bham.ac.uk><mailto:a.beggs@bham. ac.uk<mailto:a.beggs@bham.ac.uk="">>; Peter Murakami; bioconductor@r-proj ect.org<mailto:bioconductor@r-project.org><mailto:bioconductor@r-proje ct.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@bioc onductor.org=""><mailto:guest@bioconductor.org<mailto:guest@bioconductor. org="">>> To: bioconductor@r-project.org<mailto:bioconductor@r-project.org><mail to:bioconductor@r-project.org<mailto:bioconductor@r-project.org="">>, a.b eggs@bham.ac.uk<mailto:a.beggs@bham.ac.uk><mailto:a.beggs@bham.ac.uk<m ailto:a.beggs@bham.ac.uk="">> Cc: charm Maintainer <pmurakam@jhsph.edu<mailto:pmurakam@jhsph.edu><ma ilto:pmurakam@jhsph.edu<mailto:pmurakam@jhsph.edu="">>> Subject: [BioC] CHARM - The following columns in sampleKey... Message-ID: <20121102082508.CDE081429FB@mamba.fhcrc.org<mailto:2012110 2082508.cde081429fb@mamba.fhcrc.org=""><mailto: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=""><http: bioconductor.org=""/>. [[alternative HTML version deleted]] _______________________________________________ Bioconductor mailing list Bioconductor@r-project.org<mailto: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]]
ADD REPLYlink written 7.0 years ago by Andrew Beggs90
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]]
ADD REPLYlink written 7.0 years ago by P. Murakami30
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]]
ADD REPLYlink written 7.0 years ago by Benilton Carvalho4.3k
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<mailto: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<mailto: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<mailto:polyphemus421@gmail.com>] > *Sent:* 02 November 2012 15:09 > *To:* Andrew Beggs > *Cc:* Andrew Jaffe; Peter Murakami; bioconductor@r-project.org<mailto: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<mailto: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<mailto:a.beggs@bham.ac.uk>] > Sent: 02 November 2012 13:42 > To: Andrew Jaffe; 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...**** > > > 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<mailto:ajaffe@jhsph.edu>] > Sent: 02 November 2012 13:07**** > > To: a.beggs@bham.ac.uk<mailto:a.beggs@bham.ac.uk><mailto:a.beggs@bha m.ac.uk<mailto:a.beggs@bham.ac.uk="">>; Peter Murakami; > bioconductor@r-project.org<mailto:bioconductor@r-project.org><mailto :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><mailto:> guest@bioconductor.org<mailto:guest@bioconductor.org>>> > To: bioconductor@r-project.org<mailto:bioconductor@r-project.org><ma ilto:bioconductor@r-project.org<mailto:bioconductor@r-project.org="">>, > a.beggs@bham.ac.uk<mailto:a.beggs@bham.ac.uk><mailto:a.beggs@bham.ac .uk<mailto:a.beggs@bham.ac.uk="">> > Cc: charm Maintainer <pmurakam@jhsph.edu<mailto:pmurakam@jhsph.edu>< mailto:pmurakam@jhsph.edu<mailto:pmurakam@jhsph.edu>>> > Subject: [BioC] CHARM - The following columns in sampleKey... > Message-ID: <20121102082508.CDE081429FB@mamba.fhcrc.org<mailto:20121 102082508.cde081429fb@mamba.fhcrc.org=""><mailto:> 20121102082508.CDE081429FB@mamba.fhcrc.org<mailto:20121102082508.cde 081429fb@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="">< > http://bioconductor.org/>. > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org<mailto: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<mailto: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]]
ADD REPLYlink written 7.0 years ago by Andrew Beggs90
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]]
ADD REPLYlink written 7.0 years ago by Benilton Carvalho4.3k
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<mailto: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<mailto:beniltoncarvalho@gmail.com>] Sent: 05 November 2012 18:09 To: P. Murakami Cc: Andrew Beggs; Andrew Jaffe; Peter Murakami; bioconductor@r-project.org<mailto: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<mailto: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<mailto: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<mailto:polyphemus421@gmail.com>] > *Sent:* 02 November 2012 15:09 > *To:* Andrew Beggs > *Cc:* Andrew Jaffe; Peter Murakami; bioconductor@r-project.org<mailto: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<mailto: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<mailto:a.beggs@bham.ac.uk>] > Sent: 02 November 2012 13:42 > To: Andrew Jaffe; 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...**** > > > 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<mailto:ajaffe@jhsph.edu>] > Sent: 02 November 2012 13:07**** > > To: a.beggs@bham.ac.uk<mailto:a.beggs@bham.ac.uk><mailto:a.beggs@bha m.ac.uk<mailto:a.beggs@bham.ac.uk="">>; Peter Murakami; > bioconductor@r-project.org<mailto:bioconductor@r-project.org><mailto :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><mailto:> guest@bioconductor.org<mailto:guest@bioconductor.org>>> > To: bioconductor@r-project.org<mailto:bioconductor@r-project.org><ma ilto:bioconductor@r-project.org<mailto:bioconductor@r-project.org="">>, > a.beggs@bham.ac.uk<mailto:a.beggs@bham.ac.uk><mailto:a.beggs@bham.ac .uk<mailto:a.beggs@bham.ac.uk="">> > Cc: charm Maintainer <pmurakam@jhsph.edu<mailto:pmurakam@jhsph.edu>< mailto:pmurakam@jhsph.edu<mailto:pmurakam@jhsph.edu>>> > Subject: [BioC] CHARM - The following columns in sampleKey... > Message-ID: <20121102082508.CDE081429FB@mamba.fhcrc.org<mailto:20121 102082508.cde081429fb@mamba.fhcrc.org=""><mailto:> 20121102082508.CDE081429FB@mamba.fhcrc.org<mailto:20121102082508.cde 081429fb@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="">< > http://bioconductor.org/>. > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org<mailto: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<mailto: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]]
ADD REPLYlink written 7.0 years ago by Andrew Beggs90
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<mailto: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<mailto:beniltoncarvalho@gmail.com>] Sent: 05 November 2012 18:09 To: P. Murakami Cc: Andrew Beggs; Andrew Jaffe; Peter Murakami; bioconductor@r-project.org<mailto: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<mailto: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<mailto: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<mailto:polyphemus421@gmail.com>] > *Sent:* 02 November 2012 15:09 > *To:* Andrew Beggs > *Cc:* Andrew Jaffe; Peter Murakami; bioconductor@r-project.org<mailto: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<mailto: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<mailto:a.beggs@bham.ac.uk>] > Sent: 02 November 2012 13:42 > To: Andrew Jaffe; 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...**** > > > 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<mailto:ajaffe@jhsph.edu>] > Sent: 02 November 2012 13:07**** > > To: a.beggs@bham.ac.uk<mailto:a.beggs@bham.ac.uk><mailto:a.beggs@bha m.ac.uk<mailto:a.beggs@bham.ac.uk="">>; Peter Murakami; > bioconductor@r-project.org<mailto:bioconductor@r-project.org><mailto :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><mailto:> guest@bioconductor.org<mailto:guest@bioconductor.org>>> > To: bioconductor@r-project.org<mailto:bioconductor@r-project.org><ma ilto:bioconductor@r-project.org<mailto:bioconductor@r-project.org="">>, > a.beggs@bham.ac.uk<mailto:a.beggs@bham.ac.uk><mailto:a.beggs@bham.ac .uk<mailto:a.beggs@bham.ac.uk="">> > Cc: charm Maintainer <pmurakam@jhsph.edu<mailto:pmurakam@jhsph.edu>< mailto:pmurakam@jhsph.edu<mailto:pmurakam@jhsph.edu>>> > Subject: [BioC] CHARM - The following columns in sampleKey... > Message-ID: <20121102082508.CDE081429FB@mamba.fhcrc.org<mailto:20121 102082508.cde081429fb@mamba.fhcrc.org=""><mailto:> 20121102082508.CDE081429FB@mamba.fhcrc.org<mailto:20121102082508.cde 081429fb@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="">< > http://bioconductor.org/>. > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org<mailto: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<mailto: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]]
ADD REPLYlink written 6.9 years ago by Andrew Beggs90
:-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 itÂ’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]]
ADD REPLYlink written 6.9 years ago by Benilton Carvalho4.3k
Answer: CHARM - The following columns in sampleKey...
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gravatar for Martin Aryee
7.0 years ago by
Martin Aryee20
Boston, MA, USA
Martin Aryee20 wrote:
Hi Andrew, One of the things readCharm does is match up the two channel files (_532 and _635) for each sample. The input to readCharm is file- centric (i.e. two files per sample), and the output is sample-centric. When annotating samples it tries to keep as many columns of the sample description file (sampleKey) you give it as possible. A requirement for this is that the values in a given column must be identical for a given green channel file and its matching red channel file. The warning ("The following columns in sampleKey contain discrepant values between channels and are being removed") means that this is not the case. You could take a look in column 1 and see if there is a discrepancy for one or more samples. (If you don't care to keep the information in column 1 you can safely ignore the warning.) Best, Martin Martin Aryee Departments of Pathology Massachusetts General Hospital & Harvard Medical School 149 13th Street, Room 6016 Charlestown, Massachusetts 02129 Telephone: 617-726-5695 Fax: 617-726-5684 Email: aryee.martin at mgh.harvard.edu On Nov 2, 2012, at 7:00 AM, guest at bioconductor.org wrote: > > > From: "Andrew Beggs [guest]" <guest at="" bioconductor.org=""> > Subject: [BioC] CHARM - The following columns in sampleKey... > Date: November 2, 2012 4:25:08 AM EDT > To: bioconductor at r-project.org, a.beggs at bham.ac.uk > Cc: charm Maintainer <pmurakam at="" jhsph.edu=""> > > > > 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. > > > > The information in this e-mail is intended only for the ...{{dropped:11}}
ADD COMMENTlink written 7.0 years ago by Martin Aryee20
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