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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