[R] exonmap question: rma (or justplier) crashes

[Henrik Bengtsson]

Hi,

this is clearly a Bioconductor-specific issue.  Please post your
question to the Bioconductor mailing list instead.

/Henrik

On Mon, Aug 18, 2008 at 12:20 AM, Tae-Hoon Chung <hoontaechung at gmail.com> wrote:
> Hi, All;
>
> I simply followed the exonmap vignette  but came up with an unexpected
> error.
> Here are what I did:
>
>> library(exonmap)
> Loading required package: affy
> Loading required package: Biobase
> Loading required package: tools
>
> Welcome to Bioconductor
>
>  Vignettes contain introductory material. To view, type
>  'openVignette()'. To cite Bioconductor, see
>  'citation("Biobase")' and for packages 'citation(pkgname)'.
>
> Loading required package: affyio
> Loading required package: preprocessCore
> Loading required package: simpleaffy
> Loading required package: genefilter
> Loading required package: survival
> Loading required package: splines
> Loading required package: gcrma
> Loading required package: matchprobes
> Loading required package: RColorBrewer
> Loading required package: RMySQL
> Loading required package: DBI
> Loading required package: plier
>
>> raw <- read.exon(covdesc='design.csv')
>> raw at cdfName <- "exon.pmcdf"
>> dat.rma <- rma(raw)
> Error in .local(object, ...) : subscript out of bounds
>> sessionInfo()
> R version 2.7.2 beta (2008-08-16 r46368)
> i386-apple-darwin9.4.0
>
> locale:
> C
>
> attached base packages:
> [1] splines   tools     stats     graphics  grDevices utils     datasets
> [8] methods   base
>
> other attached packages:
>  [1] exon.pmcdf_1.1       exonmap_1.6.05       plier_1.8.0
>  [4] RMySQL_0.6-0         DBI_0.2-4            RColorBrewer_1.0-2
>  [7] simpleaffy_2.14.05   gcrma_2.12.1         matchprobes_1.12.0
> [10] genefilter_1.20.0    survival_2.34-1      affy_1.16.0
> [13] preprocessCore_1.0.0 affyio_1.6.1         Biobase_2.0.1
>
> loaded via a namespace (and not attached):
> [1] AnnotationDbi_1.0.6 RSQLite_0.6-4       annotate_1.18.0
>
> Thanks in advance;
>
> Tae-Hoon
>
> --
> Tae-Hoon Chung
>
> Korea Centers for Disease Control & Prevention (KCDC)
> Korea National Institute of Health
> Center for Genome Sciences :: Biobank Team
>
> (T) +82-2-380-2252
> (F) +82-2-354-1078
> (M) +82-10-3511-1012
>
>        [[alternative HTML version deleted]]
>
> ______________________________________________
> R-help at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>