[BioC] Bioconductor - hugene10stv1cdf not available

[Benilton Carvalho]

btw, if you want to use the affy package, I believe that the package:

http://www.bioconductor.org/packages/release/data/annotation/html/hugene10stv1.r3cdf.html

should suffice (you will need to specify the name of the package to be
used though, check the docs for ReadAffy).

b

On Mon, Apr 19, 2010 at 1:48 AM, Benilton Carvalho
<beniltoncarvalho at gmail.com> wrote:
> Hi Christoph,
>
> the way to do this with oligo is:
>
> library(oligo)
> rawData = read.celfiles(list.celfiles())
> summaries1 = rma(rawData, target="probeset")
> summaries2 = rma(rawData, target="core")
>
> summaries1 will contain the rma summaries to the probeset defined in
> the PGF file. summaries2 will contain the summaries for the
> metaprobesets defined in the core.mps file.
>
> AffyBatch objects are to be used with the affy package, so that's why
> the pd.hugene package was of no use (b/c pd.hugene is to be used with
> oligo).
>
> hth,
> b
>
> On Mon, Apr 19, 2010 at 1:33 AM, Christoph Knapp
> <mkna005 at aucklanduni.ac.nz> wrote:
>> 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
>>>>>
>>>>> _______________________________________________
>>>>> Bioconductor mailing list
>>>>> Bioconductor at stat.math.ethz.ch
>>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>>>>> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
>>>>>
>>>>
>>>
>>
>