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]]