[BioC] Bioconductor - hugene10stv1cdf not available

[Christoph Knapp]

I forgot to mention that I tried that as well:

>     biocLite("hugene10stv1cdf")
Using R version 2.10.1, biocinstall version 2.5.10.
Installing Bioconductor version 2.5 packages:
[1] "hugene10stv1cdf"
Please wait...

Warning message:
In getDependencies(pkgs, dependencies, available, lib) :
  package ‘hugene10stv1cdf’ is not available

Why is it not possible for me to install that package.

Thanks

Christoph

On 19 April 2010 12:13, Christoph Knapp <mkna005 at aucklanduni.ac.nz> wrote:
> Sorry,
> still no change
>
> 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)
>
> Christoph
>
> On 19 April 2010 11:51, Benilton Carvalho <beniltoncarvalho at gmail.com> wrote:
>> 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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>>>
>>
>