[BioC] Bioconductor - hugene10stv1cdf not available

[Benilton Carvalho]

the pd.hugene package (which I'd expect you to download from BioC) is
to be used with the oligo package.

b

On Sun, Apr 18, 2010 at 11:51 PM, Christoph Knapp
<mkna005 at aucklanduni.ac.nz> wrote:
> Hi all,
> I'm trying for quite some time to get an analysis started. I keep
> getting this Error.
>
> Error in getCdfInfo(object) :
>  Could not obtain CDF environment, problems encountered:
> Specified environment does not contain HuGene-1_0-st-v1
> Library - package hugene10stv1cdf not installed
> Bioconductor - hugene10stv1cdf not available
> Calls: rma ... .local -> indexProbes -> indexProbes -> .local -> getCdfInfo
> Execution halted
>
> I installed all possible packages from there
>
> http://www.bioconductor.org/docs/workflows/oligoarrays/
>
> and even downloaded and installed that one
>
> http://mbi00206.bio.med.uni-muenchen.de/free/pd.hugene.1.0.st.v1.zip)
>
> still no change.
>
> What am I missing?
>
> It reads in the CEL files
>
> VFdata=ReadAffy()
>
> but when I look at the VFdata object it already says
>
>> VFdata
> AffyBatch object
> size of arrays=1050x1050 features (11 kb)
> cdf=HuGene-1_0-st-v1 (??? affyids)
> number of samples=7
> Error in getCdfInfo(object) :
>  Could not obtain CDF environment, problems encountered:
> Specified environment does not contain HuGene-1_0-st-v1
> Library - package hugene10stv1cdf not installed
> Bioconductor - hugene10stv1cdf not available
> In addition: Warning message:
> missing cdf environment! in show(AffyBatch)
>
> and going on
>
>> eset = exprs(rma(VFdata))
> Error in getCdfInfo(object) :
>  Could not obtain CDF environment, problems encountered:
> Specified environment does not contain HuGene-1_0-st-v1
> Library - package hugene10stv1cdf not installed
> Bioconductor - hugene10stv1cdf not available
> Error in exprs(rma(VFdata)) :
>  error in evaluating the argument 'object' in selecting a method for
> function 'exprs'
>>
>
> I'm very inexperienced in terms of stuff like that. A answer for
> dummies would be much appreciated.
>
> Thanks
>
> Christoph
>
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