Minfi "mapToGenome" error when attempting to generate a genomicRatioSet
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@kasper-daniel-hansen-2979
Last seen 11 weeks ago
United States
Sorry, this took forever. Bug is fixed in minfi 1.9.11 in Bioc devel. I commit it to the minfi GitHub repos, so we'll see if it works ... And btw., it would have been fine bugging me about this. Best, Kasper On Thu, Jan 30, 2014 at 11:08 PM, Dale Watkins <dale.watkins@sahmri.com>wrote: > Thanks Kasper, much appreciated. > > Cheers, > Dale > > > From: Kasper Daniel Hansen <kasperdanielhansen@gmail.com> > Date: Friday, 31 January 2014 2:32 pm > To: Dale Watkins <dale.watkins@sahmri.com> > Cc: "bioconductor@r-project.org" <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>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]]
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Dale Watkins ▴ 30
@dale-watkins-6366
Last seen 7.1 years ago
Thanks Kasper! I really appreciate all the work you have done with minfi, it's helping me immensely with my work, and it's free, so I didn't want to be rude and bug you. Thanks again, Dale From: Kasper Daniel Hansen <kasperdanielhansen@gmail.com<mailto:kasperdanielhansen@gmail.com>> Date: Tuesday, 18 February 2014 3:12 am 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 Sorry, this took forever. Bug is fixed in minfi 1.9.11 in Bioc devel. I commit it to the minfi GitHub repos, so we'll see if it works ... And btw., it would have been fine bugging me about this. Best, Kasper On Thu, Jan 30, 2014 at 11:08 PM, Dale Watkins <dale.watkins@sahmri.com<mailto:dale.watkins@sahmri.com>> wrote: 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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For bug reports just remind me. If it takes this long, it is because I have forgotten about it. If I am too busy I have no trouble ignoring users :) Kasper On Mon, Feb 17, 2014 at 4:48 PM, Dale Watkins <dale.watkins@sahmri.com>wrote: > Thanks Kasper! > > I really appreciate all the work you have done with minfi, it's helping > me immensely with my work, and it's free, so I didn't want to be rude and > bug you. > > Thanks again, > Dale > > > From: Kasper Daniel Hansen <kasperdanielhansen@gmail.com> > Date: Tuesday, 18 February 2014 3:12 am > > To: Dale Watkins <dale.watkins@sahmri.com> > Cc: "bioconductor@r-project.org" <bioconductor@r-project.org> > Subject: Re: [BioC] Minfi "mapToGenome" error when attempting to generate > a genomicRatioSet > > Sorry, this took forever. Bug is fixed in minfi 1.9.11 in Bioc devel. > I commit it to the minfi GitHub repos, so we'll see if it works ... > > And btw., it would have been fine bugging me about this. > > Best, > Kasper > > > On Thu, Jan 30, 2014 at 11:08 PM, Dale Watkins <dale.watkins@sahmri.com>wrote: > >> Thanks Kasper, much appreciated. >> >> Cheers, >> Dale >> >> >> From: Kasper Daniel Hansen <kasperdanielhansen@gmail.com> >> Date: Friday, 31 January 2014 2:32 pm >> To: Dale Watkins <dale.watkins@sahmri.com> >> Cc: "bioconductor@r-project.org" <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>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]]
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diana0690 • 0
@diana0690-9113
Last seen 5.9 years ago
Netherlands

Hi all,

I have a new problem with the mapToGenome function in Minfi. 

I have been working with minfi for a while now and made script according to the minfi tutorial.

Everything worked fine, but since a week or so, I get the following error when using this command

>gset <- mapToGenome(ratioSet)

>Error in getAnnotation(object, what = what, dropNonMapping = TRUE, orderByLocation = orderByLocation,  : 
  the value of argument 'what' is not part of the annotation package or 'everything'

I have tried multiple things, but everytime I get the same error.

What it going wrong?

Diana

 

 

> sessionInfo()
R version 3.2.2 (2015-08-14)
Platform: i386-w64-mingw32/i386 (32-bit)
Running under: Windows 7 (build 7601) Service Pack 1

locale:
[1] LC_COLLATE=Dutch_Netherlands.1252  LC_CTYPE=Dutch_Netherlands.1252   
[3] LC_MONETARY=Dutch_Netherlands.1252 LC_NUMERIC=C                      
[5] LC_TIME=Dutch_Netherlands.1252    

attached base packages:
[1] stats4    parallel  stats     graphics  grDevices utils     datasets 
[8] methods   base     

other attached packages:
 [1] ChAMP_1.8.0                                       
 [2] Illumina450ProbeVariants.db_1.6.0                 
 [3] ChAMPdata_1.8.0                                   
 [4] FlowSorted.Blood.450k_1.8.0                       
 [5] IlluminaHumanMethylation450kmanifest_0.4.0        
 [6] wateRmelon_1.10.0                                 
 [7] IlluminaHumanMethylation450kanno.ilmn12.hg19_0.2.1
 [8] ROC_1.46.0                                        
 [9] lumi_2.22.0                                       
[10] methylumi_2.16.0                                  
[11] FDb.InfiniumMethylation.hg19_2.2.0                
[12] org.Hs.eg.db_3.2.3                                
[13] RSQLite_1.0.0                                     
[14] DBI_0.3.1                                         
[15] TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2           
[16] GenomicFeatures_1.22.2                            
[17] AnnotationDbi_1.32.0                              
[18] ggplot2_1.0.1                                     
[19] reshape2_1.4.1                                    
[20] scales_0.3.0                                      
[21] matrixStats_0.15.0                                
[22] limma_3.26.1                                      
[23] minfi_1.16.0                                      
[24] bumphunter_1.10.0                                 
[25] locfit_1.5-9.1                                    
[26] iterators_1.0.8                                   
[27] foreach_1.4.3                                     
[28] Biostrings_2.38.0                                 
[29] XVector_0.10.0                                    
[30] SummarizedExperiment_1.0.0                        
[31] GenomicRanges_1.22.0                              
[32] GenomeInfoDb_1.6.0                                
[33] IRanges_2.4.1                                     
[34] S4Vectors_0.8.0                                   
[35] lattice_0.20-33                                   
[36] Biobase_2.30.0                                    
[37] BiocGenerics_0.16.0                               
[38] metafor_1.9-8                                     
[39] Matrix_1.2-2                                      

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.1             cluster_2.0.3           magrittr_1.5           
 [4] MASS_7.3-43             GenomicAlignments_1.6.1 splines_3.2.2          
 [7] zlibbioc_1.16.0         mclust_5.1              beanplot_1.2           
[10] impute_1.44.0           ellipse_0.3-8           xtable_1.8-0           
[13] colorspace_1.2-6        quadprog_1.5-5          doRNG_1.6              
[16] nor1mix_1.2-1           GEOquery_2.36.0         futile.logger_1.4.1    
[19] genefilter_1.52.0       lambda.r_1.1.7          siggenes_1.44.0        
[22] digest_0.6.8            multtest_2.26.0         preprocessCore_1.32.0  
[25] nleqslv_2.9             RCurl_1.95-4.7          pheatmap_1.0.7         
[28] BiocInstaller_1.20.0    Rsamtools_1.22.0        reshape_0.8.5          
[31] annotate_1.48.0         igraph_1.0.1            DNAcopy_1.44.0         
[34] munsell_0.4.2           BiocParallel_1.4.0      pkgmaker_0.22          
[37] plyr_1.8.3              stringr_1.0.0           tools_3.2.2            
[40] rngtools_1.2.4          grid_3.2.2              base64_1.1             
[43] nlme_3.1-121            gtable_0.1.2            mgcv_1.8-7             
[46] KernSmooth_2.23-15      marray_1.48.0           affy_1.48.0            
[49] registry_0.3            rgl_0.95.1367           survival_2.38-3        
[52] RPMM_1.20               affyio_1.40.0           sva_3.18.0             
[55] rtracklayer_1.30.1      RColorBrewer_1.1-2      bitops_1.0-6           
[58] codetools_0.2-14        futile.options_1.0.0    mixOmics_5.1.2         
[61] biomaRt_2.26.0          stringi_1.0-1           XML_3.98-1.3           
[64] illuminaio_0.12.0       proto_0.3-10 

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