[R] normalizing affy data caused an error

Sat Apr 28 15:07:54 CEST 2007

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

 > 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"