[BioC] gcrma and combineAffyBatch

[Lo, Ken]

Hi all, 
 
As I am a newbie to the bioconductor world, I would like to ask a
question that Zhijin Wu and Vincent has touched upon.  I would like to
use combineAffyBatch to combine a set of U133A and U133Plus2 expression
arrays.  I have done that sucessfully with combineAffyBatch and ran RMA
on the combined dataset sucessfully.  However, when I tried running
gcrma on the combined dataset, it throws an error:
 
Adjusting for optical effect.....Done.
Computing affinities[1] "Checking to see if your internet connection
works..."
[1] "Environment tempcdfcdf was not found in the Bioconductor
repository."
[1] "Checking to see if your internet connection works..."
[1] "Environment tempcdfprobe was not found in the Bioconductor
repository."
Error in get(x, envir, mode, inherits) : variable "tempcdfprobe" was not
found

I tried applying the solution that was provided by Wu (in response to
Vincent Detours) but failed as the dimensions of the 
 
affinity.info1=new("AffyBatch",
exprs=exprs(affinity.info1),cdfname(affinity.info1), nrow=640, ncol=640)

 
statement is not right for the U133A and U133Plus2 platform.  Would
anyone be able to guide me to do this?
 
Best regards,
 
Ken Lo
 

**********************************************

Ken Lo, PhD
Post-Doctorate Fellow
Department of Cancer Genetics
Center for Genetics and Pharmacology
Roswell Park Cancer Institute
Elm and Carlton Streets
Buffalo, New York 14263
Telephone:  716-845-3941
Fax:         716-845-3940
E-mail:      Ken.Lo at RoswellPark.org
Web:        www.RoswellPark.org <http://www.roswellpark.org/>  
 
Located in the
Buffalo Life Science Complex
on the Buffalo Niagara Medical Campus

**********************************************



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