[BioC] Bioconductor - hugene10stv1cdf not available

[Christoph Knapp]

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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>