[BioC] Bioconductor - hugene10stv1cdf not available

[Benilton Carvalho]

Hi Christoph,

If you need AffyBatch objects, you'll need to stick with the affy package.

The affy and oligo packages try to extract the annotation package name
from the CEL files and automagically install these packages. But when
Affymetrix releases new revisions of the PGF/CDF files, the names of
the annotation packages are likely to change (to reflect the revision
number). The CEL files, on the other hand, remain the same (this is
why you're having "problems").

Sorry if our solution isn't very useful for you, but I hope this
clarifies what's going on.

Best wishes,

benilton

On Mon, Apr 19, 2010 at 4:52 AM, Christoph Knapp
<mkna005 at aucklanduni.ac.nz> wrote:
> Thats very complicated and (Sorry) in my case not very useful. My
> program needs to be able to read a great range of CEL files and
> schould end up with the same object preferable an AFFYbatch object (or
> I have to rewrite all my code). I need a standard way to read CEL
> files were the user is not concerned about the micro-array chip type
> used to get the CEL files. Is that possible?
>
> Thank you very much for your reply though.
>
> Christoph
>
> On 19 April 2010 12:51, Benilton Carvalho <beniltoncarvalho at gmail.com> wrote:
>> 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
>>>>>>>
>>>>>>> _______________________________________________
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>>>>>>> Bioconductor at stat.math.ethz.ch
>>>>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor
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>>>>>>>
>>>>>>
>>>>>
>>>>
>>>
>>
>