[BioC] problem with 2.0 cdf

[Joern Toedling]

Hello,

how are you reading in the cel-files? The functions ReadAffy or read.affybatch
from package "affy" normally should be able to determine the microarray type
and set the cdfName slot of the AffyBatch object correctly. Both also have an
argument 'cdfName' which can be used to specify alternative CDF environments.

So a dirty hack to "repair" your AffyBatch object would be specifying
data at cdfName <- "hgu133plus2"

However, I think you should investigate why that information was not in your
AffyBatch in the first place.

And please always specify the sessionInfo() output when asking questions to
this list, such that the maintainers of package "affy" can see which version
of the package you are using.

Regards,
Joern

On Fri, 10 Jul 2009 12:57:43 +0200, Alberto Goldoni wrote
> Dear all,
> 
> I have 15 cel file and all is good until i try to normalize the dataset:
> 
> data.rma<rma(data)
> 
> Error in getCdfInfo(object) :
>   Could not obtain CDF environment, problems encountered:
> Specified environment does not contain 2.0
> Library - package 2.0cdf not installed
> Bioconductor - 2.0cdf not available
> 
> > data
> AffyBatch object
> size of arrays=1164x1164 features (9 kb)
> cdf=2.0 (??? affyids)
> number of samples=15
> Errore in getCdfInfo(object) :
>   Could not obtain CDF environment, problems encountered:
> Specified environment does not contain 2.0
> Library - package 2.0cdf not installed
> Bioconductor - 2.0cdf not available
> 
> why it gives to me this kind of error?
> I'm using HG-U133_Plus_2_1_1.CEL file and the package hgu133plus2,
> hgu133plus2cdf and hgu133plus2probe are correctly installed.
> 
> Someone can help me?
> 
> Best regards.
> 
> -- 
> -----------------------------------------------------
> Dr. Alberto Goldoni
> Bologna, Italy
> -----------------------------------------------------