Hi,
It looks like the issue is happening somewhere in rma() - or something it
doesn¹t like in the Oraw¹ data object... There¹s a more recent version of
the affy library than the one you¹re using, I think. Please can you try
updating that and seeing if it fixes things?

Crispin

On 19/8/08 09:15, "" <> 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@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]]
> 
> _______________________________________________
> Bioconductor mailing list
> Bioconductor@stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives:
> http://news.gmane.org/gmane.science.biology.informatics.conductor
> 
--------------------------------------------------------
This email is confidential and intended solely for the u...{{dropped:15}}