
Hi Ken,

I have had the same problem two weeks ago, and I'll try to let you benefit 
from my experience.
First, you should check that the combined affybatch you have created is 
really associated with the cdf environment that is reported as missing by 
gcrma().
You can do that with :
> cdfName(the_name_of_your_affybatch)
If it does not return tempcdfcdf (I assume that the latter is the name of 
the newly created cdf env), then you can set it with :
> the_name_of_your_affybatch@cdfName <- "tempcdfcdf"

Now, the probe file is also missing for gcrma(), and for that I have no 
specific solution; as a workaround, what I did was to run the gcrma 
background correction only (use bg.adjust.gcrma ) on the two separate 
affybatches ( I understand that, for each sample, the background 
correction is independent of the other samples), then I combined the 
background corrected affybatches, and then I ran the normalization and 
summarization steps with rma(the_name_of_your_affybatch,background=FALSE).

I hope that it will help !

Jean-Louis

----------------------------------
Jean-Louis Ruelle
GlaxoSmithKline Biologicals, R&D
Belgium
Phone : + 32-2-6568451
Fax :   +32-2-6568436
email :  jean-louis.ruelle@gskbio.com





"Lo, Ken" <Ken.Lo@roswellpark.org> 
Sent by: bioconductor-bounces@stat.math.ethz.ch
05-Oct-2006 23:06
 
To
<bioconductor@stat.math.ethz.ch>
cc

Subject
[BioC] gcrma and combineAffyBatch






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@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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