Hello,

please keep this correspondence on the BioC list for allowing other people to contribute and to have them in the searchable archive.

My suggested "hack" was meant as a reply to your source code that did not work, so I assumed there already is an AffyBatch object called 'data'. If you don't have such an object, 'data' will refer to a basic R function with that name. This is the reason why 'data' is actually not a good name for your object. So in detail, my suggestion was to create a working AffyBatch object, for example named 'A', from your CEL files by either
A <- ReadAffy(<other arguments, see ?ReadAffy>, cdfName="hgu133plus2")
# or by first creating an AffyBatch object by any other way you prefer:
A <- ...
stopifnot(inherits(A, "AffyBatch"))
A@cdfName <- "hgu133plus2"

The first way is usually preferable.

Regards,
Joern

PS: when you provide sessionInfo() output, please provide the full output, as we need to know the version of R and the versions of all attached packages.

On Fri, 10 Jul 2009 13:58:05 +0200, Alberto Goldoni wrote
> i have tryed but with no success
> 
> data@cdfName <- "hgu133plus2"
> Error in checkSlotAssignment(object, name, value) : 
>   "cdfName" is not a slot in class "function"
> 
> > sessionInfo()
> R version 2.9.1 (2009-06-26) 
> i486-pc-linux-gnu 
> 
> 2009/7/10 Joern Toedling <Joern.Toedling@curie.fr>
> 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@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

 

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