[BioC] CEL files not valid?

[James F. Reid]

Hi,

use full.names=TRUE in your list.files call to get the full path to your 
files.

J.

On 06/14/2011 06:54 PM, array chip wrote:
> I figured it out, I need to start R session in the directory where the cel files
> are stored.
>
>
>
>
> ________________________________
>
> To: bioconductor at r-project.org
> Sent: Tue, June 14, 2011 9:41:05 AM
> Subject: [BioC] CEL files not valid?
>
> Hi I downloaded GSE2034 dataset from GEO. But when I tried to read in these cel
> files using ReadAffy(), I got the following error message:
>
>> library(affy)
>> fls<-list.files("my directory to CEL files", ".*cel")## get cell files
>> aBatch<-ReadAffy(filenames=fls)## input raw CEL files
> Error: the following are not valid files:
>      GSM177885.cel
>     GSM177886.cel
>     GSM177887.cel
>     GSM177888.cel
> :
> :
>
> Anyone has any suggestions what is going on?
>
>> sessionInfo()
> R version 2.12.2 (2011-02-25)
> Platform: i386-pc-mingw32/i386 (32-bit)
>
> locale:
> [1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United
> States.1252    LC_MONETARY=English_United States.1252
> [4] LC_NUMERIC=C                           LC_TIME=English_United States.1252
>
>
>
> attached base packages:
> [1] stats     graphics  grDevices datasets  utils     methods   base
>
> other attached packages:
> [1] affy_1.28.1    Biobase_2.10.0 rcom_2.2-3.1   rscproxy_1.3-1
>
> loaded via a namespace (and not attached):
> [1] affyio_1.18.0         preprocessCore_1.12.0 tools_2.12.2
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