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)

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