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

[Rob Dunne]

Hi Crespin,

Crispin Miller wrote:
> Hi Rob,
> That's curious...
>   
yes. It only happens with my data set. I just tried the Rat exon data 
set from the
Affymetrix site with no problems.


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

 > sessionInfo()
R version 2.6.2 (2008-02-08)
x86_64-unknown-linux-gnu

locale:
LC_CTYPE=en_AU.UTF-8;LC_NUMERIC=C;LC_TIME=en_AU.UTF-8;LC_COLLATE=en_AU.UTF-8;
LC_MONETARY=en_AU.UTF-8;LC_MESSAGES=en_AU.UTF-8;
LC_PAPER=en_AU.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;
LC_MEASUREMENT=en_AU.UTF-8;LC_IDENTIFICATION=C

attached base packages:
[1] splines   tools     stats     graphics  grDevices utils     datasets
[8] methods   base    

other attached packages:
 [1] ratexonpmcdf_1.1     exonmap_1.4.3        plier_1.8.0        
 [4] RMySQL_0.6-0         DBI_0.2-4            RColorBrewer_1.0-2 
 [7] simpleaffy_2.14.05   gcrma_2.10.0         matchprobes_1.10.0 
[10] genefilter_1.16.0    survival_2.34-1      affy_1.16.0        
[13] preprocessCore_1.0.0 affyio_1.6.1         Biobase_1.16.3     

loaded via a namespace (and not attached):
[1] annotate_1.16.1     AnnotationDbi_1.0.6 RSQLite_0.6-8     
 >


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

> 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.
>>     

yes -- its just the same. If it is the data, are there any consistency 
checks I can do?
I can extract the probe values with no problem
X<-exprs(data)
 > dim(X)
[1] 1102500      59
 > any(is.na(X))
[1] FALSE

Bye
Rob




-- 
Rob Dunne         Fax: +61 2 9325 3200     Tel: +61 2 9325 3263
CSIRO Mathematical and Information Sciences     +61 2 9325 3100
Locked Bag 17, North Ryde, New South Wales, Australia, 1670
http://www.bioinformatics.csiro.au Email: Rob.Dunne at csiro.au

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