[BioC] Bioconductor - hugene10stv1cdf not available

[Christoph Knapp]

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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>>>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor
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>>>>>>
>>>>>
>>>>
>>>
>>
>