[R] normalizing affy data caused an error

Sat Apr 28 19:04:38 CEST 2007

Thomas Funke wrote:
> Hi all,
> 
> I tried to do normalization of affymetrix data with bioconductor on a 
> Linux  server. When I read in the cel files all seemed ok. But the next 
> step caused an error. With Win XP all works fine. Did anyone experience 
> similar problems?
> 
> Thanks,
> 
> Thomas

There is the Bioconductor mailing list for questions related to 
BioConductor. People on that list are more likely to be of help on 
related questions.

Best,
Uwe Ligges

> 
> 
>  > PI <- ReadAffy()
>  > PI
> AffyBatch object
> size of arrays=712x712 features (14 kb)
> cdf=ATH1-121501 (??? affyids)
> number of samples=6
> number of genes=506944
> annotation=ath1121501
> notes= Warning messages:
> 1: Line starting '<TITLE>Error</TITLE> ...' is malformed!
> 2: Line starting '<BODY> ...' is malformed!
> 3: Line starting '<H1>Error</H1> ...' is malformed!
> 4: missing cdf environment! in show(AffyBatch)
> 
> 
> 
> 
> 
>  > sessionInfo()
> R version 2.5.0 (2007-04-23)
> x86_64-unknown-linux-gnu
> 
> locale:
> LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C 
> 
> 
> attached base packages:
> [1] "tools"     "stats"     "graphics"  "grDevices" "utils"     "datasets"
> [7] "methods"   "base"   
> other attached packages:
>    affy   affyio  Biobase
> "1.14.0"  "1.4.0" "1.14.0"
> 
> 
> 
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> 
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