Minfi "mapToGenome" error when attempting to generate a genomicRatioSet

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Dale Watkins ▴ 30

@dale-watkins-6366

Last seen 10.3 years ago

Hi Kasper (and all Bioconductor users), I have been using Minfi to analyse a 450K experiment and have run into an error when I use 'mapToGenome' function that I can't understand or seem to fix. I am wanting to convert a ratioSet to a genomicRatioSet as follows: > ratioSet <- ratioConvert(MSet.swan, what = "both", keepCN = TRUE) > gRatioSet <- mapToGenome(ratioSet, mergeManifest = TRUE) But the following error occurs when attempting to generate the genomicRatioSet: > gRatioSet <- mapToGenome(ratioSet, mergeManifest = TRUE) Error in `elementMetadata<-`(`*tmp*`, value = <s4 object="" of="" class="" "dataframe"="">) : names of metadata columns cannot be one of "seqnames", "ranges", "strand", "seqlevels", "seqlengths", "isCircular", "start", "end", "width", "element" If I make "mergeManifest = FALSE" it seems to work, but then I don't get the merged genomic info, which I'm after. Is there another way of doing this that I haven't found? Traceback() and sessionInfo() as follows: > traceback() 7: stop(msg) 6: `elementMetadata<-`(`*tmp*`, value = <s4 object="" of="" class="" "dataframe"="">) 5: `elementMetadata<-`(`*tmp*`, value = <s4 object="" of="" class="" "dataframe"="">) 4: getLocations(object, mergeManifest = mergeManifest, orderByLocation = TRUE) 3: .local(object, ...) 2: mapToGenome(ratioSet, mergeManifest = TRUE) 1: mapToGenome(ratioSet, mergeManifest = TRUE) > sessionInfo() R version 3.0.2 (2013-09-25) Platform: x86_64-apple-darwin10.8.0 (64-bit) locale: [1] en_AU.UTF-8/en_AU.UTF-8/en_AU.UTF-8/C/en_AU.UTF-8/en_AU.UTF-8 attached base packages: [1] parallel stats graphics grDevices utils datasets methods base other attached packages: [1] IlluminaHumanMethylation450kanno.ilmn12.hg19_0.2.1 shinyMethyl_1.0.3 [3] RColorBrewer_1.0-5 gmodels_2.15.4.1 [5] matrixStats_0.8.14 shiny_0.8.0.99 [7] IlluminaHumanMethylation450kmanifest_0.4.0 minfi_1.8.9 [9] bumphunter_1.2.0 locfit_1.5-9.1 [11] iterators_1.0.6 foreach_1.4.1 [13] Biostrings_2.30.1 GenomicRanges_1.14.4 [15] XVector_0.2.0 IRanges_1.20.6 [17] reshape_0.8.4 plyr_1.8 [19] lattice_0.20-24 Biobase_2.22.0 [21] BiocGenerics_0.8.0 loaded via a namespace (and not attached): [1] annotate_1.40.0 AnnotationDbi_1.24.0 base64_1.1 beanplot_1.1 bitops_1.0-6 caTools_1.16 [7] codetools_0.2-8 DBI_0.2-7 digest_0.6.4 doRNG_1.5.5 gdata_2.13.2 genefilter_1.44.0 [13] grid_3.0.2 gtools_3.2.1 httpuv_1.2.1 illuminaio_0.4.0 itertools_0.1-1 limma_3.18.9 [19] MASS_7.3-29 mclust_4.2 multtest_2.18.0 nlme_3.1-113 nor1mix_1.1-4 pkgmaker_0.17.4 [25] preprocessCore_1.24.0 R.methodsS3_1.6.1 Rcpp_0.10.6 registry_0.2 RJSONIO_1.0-3 rngtools_1.2.3 [31] RSQLite_0.11.4 siggenes_1.36.0 splines_3.0.2 stats4_3.0.2 stringr_0.6.2 survival_2.37-7 [37] tools_3.0.2 XML_3.95-0.2 xtable_1.7-1 Any help or advice would be greatly appreciated. Thanks, Dale Dale Watkins, BSc (Biotech) Hons PhD Scholar Cancer Theme, South Australian Health and Medical Research Institute (SAHMRI) [[alternative HTML version deleted]]

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ADD COMMENT • link updated 10.9 years ago by Kasper Daniel Hansen ★ 6.5k • written 10.9 years ago by Dale Watkins ▴ 30

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Kasper Daniel Hansen ★ 6.5k

@kasper-daniel-hansen-2979

Last seen 18 months ago

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I can replicate. This is clearly a bug, which I will fix in the next couple of days. Best, Kasper On Wed, Jan 29, 2014 at 6:51 PM, Dale Watkins <dale.watkins@sahmri.com>wrote: > Hi Kasper (and all Bioconductor users), > > I have been using Minfi to analyse a 450K experiment and have run into an > error when I use 'mapToGenome' function that I can't understand or seem to > fix. I am wanting to convert a ratioSet to a genomicRatioSet as follows: > > > ratioSet <- ratioConvert(MSet.swan, what = "both", keepCN = TRUE) > > > gRatioSet <- mapToGenome(ratioSet, mergeManifest = TRUE) > > But the following error occurs when attempting to generate the > genomicRatioSet: > > > gRatioSet <- mapToGenome(ratioSet, mergeManifest = TRUE) > Error in `elementMetadata<-`(`*tmp*`, value = <s4 object="" of="" class=""> "DataFrame">) : > names of metadata columns cannot be one of "seqnames", "ranges", > "strand", "seqlevels", "seqlengths", "isCircular", "start", "end", "width", > "element" > > If I make "mergeManifest = FALSE" it seems to work, but then I don't get > the merged genomic info, which I'm after. Is there another way of doing > this that I haven't found? > > > Traceback() and sessionInfo() as follows: > > > traceback() > 7: stop(msg) > 6: `elementMetadata<-`(`*tmp*`, value = <s4 object="" of="" class="" "dataframe"="">) > 5: `elementMetadata<-`(`*tmp*`, value = <s4 object="" of="" class="" "dataframe"="">) > 4: getLocations(object, mergeManifest = mergeManifest, orderByLocation = > TRUE) > 3: .local(object, ...) > 2: mapToGenome(ratioSet, mergeManifest = TRUE) > 1: mapToGenome(ratioSet, mergeManifest = TRUE) > > > sessionInfo() > R version 3.0.2 (2013-09-25) > Platform: x86_64-apple-darwin10.8.0 (64-bit) > > locale: > [1] en_AU.UTF-8/en_AU.UTF-8/en_AU.UTF-8/C/en_AU.UTF-8/en_AU.UTF-8 > > attached base packages: > [1] parallel stats graphics grDevices utils datasets methods > base > > other attached packages: > [1] IlluminaHumanMethylation450kanno.ilmn12.hg19_0.2.1 shinyMethyl_1.0.3 > [3] RColorBrewer_1.0-5 gmodels_2.15.4.1 > [5] matrixStats_0.8.14 shiny_0.8.0.99 > [7] IlluminaHumanMethylation450kmanifest_0.4.0 minfi_1.8.9 > [9] bumphunter_1.2.0 locfit_1.5-9.1 > [11] iterators_1.0.6 foreach_1.4.1 > [13] Biostrings_2.30.1 > GenomicRanges_1.14.4 > [15] XVector_0.2.0 IRanges_1.20.6 > [17] reshape_0.8.4 plyr_1.8 > [19] lattice_0.20-24 Biobase_2.22.0 > [21] BiocGenerics_0.8.0 > > loaded via a namespace (and not attached): > [1] annotate_1.40.0 AnnotationDbi_1.24.0 base64_1.1 > beanplot_1.1 bitops_1.0-6 caTools_1.16 > [7] codetools_0.2-8 DBI_0.2-7 digest_0.6.4 > doRNG_1.5.5 gdata_2.13.2 genefilter_1.44.0 > [13] grid_3.0.2 gtools_3.2.1 httpuv_1.2.1 > illuminaio_0.4.0 itertools_0.1-1 limma_3.18.9 > [19] MASS_7.3-29 mclust_4.2 multtest_2.18.0 > nlme_3.1-113 nor1mix_1.1-4 pkgmaker_0.17.4 > [25] preprocessCore_1.24.0 R.methodsS3_1.6.1 Rcpp_0.10.6 > registry_0.2 RJSONIO_1.0-3 rngtools_1.2.3 > [31] RSQLite_0.11.4 siggenes_1.36.0 splines_3.0.2 > stats4_3.0.2 stringr_0.6.2 survival_2.37-7 > [37] tools_3.0.2 XML_3.95-0.2 xtable_1.7-1 > > > Any help or advice would be greatly appreciated. > > Thanks, > Dale > > Dale Watkins, BSc (Biotech) Hons > PhD Scholar > Cancer Theme, South Australian Health and Medical Research Institute > (SAHMRI) > > [[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 COMMENT • link 10.9 years ago Kasper Daniel Hansen ★ 6.5k

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Thanks Kasper, much appreciated. Cheers, Dale From: Kasper Daniel Hansen <kasperdanielhansen@gmail.com<mailto:kasperdanielhansen@gmail.com>> Date: Friday, 31 January 2014 2:32 pm To: Dale Watkins <dale.watkins@sahmri.com<mailto:dale.watkins@sahmri.com>> Cc: "bioconductor@r-project.org<mailto:bioconductor@r-project.org>" <bioconductor@r-project.org<mailto:bioconductor@r-project.org>> Subject: Re: [BioC] Minfi "mapToGenome" error when attempting to generate a genomicRatioSet I can replicate. This is clearly a bug, which I will fix in the next couple of days. Best, Kasper On Wed, Jan 29, 2014 at 6:51 PM, Dale Watkins <dale.watkins@sahmri.com<mailto:dale.watkins@sahmri.com>> wrote: Hi Kasper (and all Bioconductor users), I have been using Minfi to analyse a 450K experiment and have run into an error when I use 'mapToGenome' function that I can't understand or seem to fix. I am wanting to convert a ratioSet to a genomicRatioSet as follows: > ratioSet <- ratioConvert(MSet.swan, what = "both", keepCN = TRUE) > gRatioSet <- mapToGenome(ratioSet, mergeManifest = TRUE) But the following error occurs when attempting to generate the genomicRatioSet: > gRatioSet <- mapToGenome(ratioSet, mergeManifest = TRUE) Error in `elementMetadata<-`(`*tmp*`, value = <s4 object="" of="" class="" "dataframe"="">) : names of metadata columns cannot be one of "seqnames", "ranges", "strand", "seqlevels", "seqlengths", "isCircular", "start", "end", "width", "element" If I make "mergeManifest = FALSE" it seems to work, but then I don't get the merged genomic info, which I'm after. Is there another way of doing this that I haven't found? Traceback() and sessionInfo() as follows: > traceback() 7: stop(msg) 6: `elementMetadata<-`(`*tmp*`, value = <s4 object="" of="" class="" "dataframe"="">) 5: `elementMetadata<-`(`*tmp*`, value = <s4 object="" of="" class="" "dataframe"="">) 4: getLocations(object, mergeManifest = mergeManifest, orderByLocation = TRUE) 3: .local(object, ...) 2: mapToGenome(ratioSet, mergeManifest = TRUE) 1: mapToGenome(ratioSet, mergeManifest = TRUE) > sessionInfo() R version 3.0.2 (2013-09-25) Platform: x86_64-apple-darwin10.8.0 (64-bit) locale: [1] en_AU.UTF-8/en_AU.UTF-8/en_AU.UTF-8/C/en_AU.UTF-8/en_AU.UTF-8 attached base packages: [1] parallel stats graphics grDevices utils datasets methods base other attached packages: [1] IlluminaHumanMethylation450kanno.ilmn12.hg19_0.2.1 shinyMethyl_1.0.3 [3] RColorBrewer_1.0-5 gmodels_2.15.4.1 [5] matrixStats_0.8.14 shiny_0.8.0.99 [7] IlluminaHumanMethylation450kmanifest_0.4.0 minfi_1.8.9 [9] bumphunter_1.2.0 locfit_1.5-9.1 [11] iterators_1.0.6 foreach_1.4.1 [13] Biostrings_2.30.1 GenomicRanges_1.14.4 [15] XVector_0.2.0 IRanges_1.20.6 [17] reshape_0.8.4 plyr_1.8 [19] lattice_0.20-24 Biobase_2.22.0 [21] BiocGenerics_0.8.0 loaded via a namespace (and not attached): [1] annotate_1.40.0 AnnotationDbi_1.24.0 base64_1.1 beanplot_1.1 bitops_1.0-6 caTools_1.16 [7] codetools_0.2-8 DBI_0.2-7 digest_0.6.4 doRNG_1.5.5 gdata_2.13.2 genefilter_1.44.0 [13] grid_3.0.2 gtools_3.2.1 httpuv_1.2.1 illuminaio_0.4.0 itertools_0.1-1 limma_3.18.9 [19] MASS_7.3-29 mclust_4.2 multtest_2.18.0 nlme_3.1-113 nor1mix_1.1-4 pkgmaker_0.17.4 [25] preprocessCore_1.24.0 R.methodsS3_1.6.1 Rcpp_0.10.6 registry_0.2 RJSONIO_1.0-3 rngtools_1.2.3 [31] RSQLite_0.11.4 siggenes_1.36.0 splines_3.0.2 stats4_3.0.2 stringr_0.6.2 survival_2.37-7 [37] tools_3.0.2 XML_3.95-0.2 xtable_1.7-1 Any help or advice would be greatly appreciated. Thanks, Dale Dale Watkins, BSc (Biotech) Hons PhD Scholar Cancer Theme, South Australian Health and Medical Research Institute (SAHMRI) [[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]]

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