[BioC] Bioconductor Digest, Vol 86, Issue 19

[Sherri Christian]

Hi Christoph,

First, install the package as suggested by Benilton - the name that  
you tried was not correct

 >biocLite("hugene10stv1.r3cdf")

Then load the library

 >library("hugene10stv1.r3cdf")

Then read in your data

 >data <- ReadAffy()  #will read in all CEL files in your working  
directory

Then tell Affy which cdf file it needs to use- because the name of  
the CDF file that Affy thinks it needs is NOT what you downloaded

 >data at cdfName <- "hugene10stv1.r3cdf"

Now check your data to be sure that the correct cdf file was used

 >data


good luck,

Sherri


Date: Mon, 19 Apr 2010 01:51:17 +0100
From: Benilton Carvalho <beniltoncarvalho at gmail.com>
To: Christoph Knapp <mkna005 at aucklanduni.ac.nz>
Cc: bioconductor at stat.math.ethz.ch
Subject: Re: [BioC] Bioconductor - hugene10stv1cdf not available
Message-ID:
	<v2se71a39ea1004181751p8be0629cnb483027cda4c1b95 at mail.gmail.com>
Content-Type: text/plain; charset=windows-1252

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