[BioC] rma subscript out of bounds with Rat Exon data

[Crispin Miller]

Hi Rob,
That's curious...

Please can you let us know which versions of the software you're running
with a call to:

> sessionInfo()

-- and what platform (i.e. Linux, Windows, Mac OS X ...) you're running on.

Do you get the same error if you call read.exon() from the directory with
your data in -- and without the compress parameter-- ie, something like:

> setwd("/home/bioinfo/RatDiet")
> data <- read.exon()
> .. etc.

Crispin






On 24/4/08 08:19, "Rob Dunne" <rob.dunne at csiro.au> wrote:

> 
> Hello Bioconductor list,
> 
>       I get an error when I try to rma normalize a data set of
> Rat Exon 1.0 ST cel files i.e.
> 
> library(exonmap)
> library(ratexonpmcdf) # Rat Exon 1.0ST from
> #http://xmap.picr.man.ac.uk/download/
> 
> data<-read.exon(path="/home/bioinfo/RatDiet/",compress=TRUE)
> data at cdfName
> #[1] "RaGene-1_0-st-v1"
> data at cdfName <- "ratexonpmcdf"
> X<-rma(data)
> #Error in .local(object, ...) : subscript out of bounds
> 
> length(probeNames(data)) #3999056
> length(data)             #59
> length(geneNames(data))  #1018777
> 
> The problem occurs in the "pm" function where it appears that
> an index is generated that is much larger than the matrix of
> expression values.
> 
> I have no problems with the human array tutorial example provided at
> http://bioinformatics.picr.man.ac.uk/
> 
> 
> Bye
> Rob
> 
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