[BioC] Bioconductor - hugene10stv1cdf not available

[Christoph Knapp]

Now I'm getting following error. This chip type gives me a headache
and if I go on probably gastric ulcer to.

Error in setQCEnvironment(cdfn) :
  Could not find array definition file ' hugene10stv1.r3cdf.qcdef '.
Simpleaffy does not know the QC parameters for this array type.
See the package vignette for details about how to specify QC
parameters manually.
Calls: qc -> qc -> qc.affy -> setQCEnvironment
Execution halted

This happens in

QCReport(VFdata,file=paste(totalJobpath,"\\","AffyQCReport.pdf",sep=""))

It generates some of the report but not all.

I tried

setQCEnvironment(cleancdfname(cdfName(eset)))

as suggested in

http://127.0.0.1:25446/library/simpleaffy/html/setQCEnvironment.html

but that did not help.

Please help?

Christoph

On 20 April 2010 11:03, Sherri Christian <sherri at mun.ca> wrote:
> Christoph,
>
> I do not have a lot of experience with Bioconductor but my experience is
> that for some chips (ie. mouse4302), the information is retrieved
> automatically but for the hugene10 chip it is not. My understanding is that
> it is because of the syntax of the file that is suggested by the CEL file
> (this is what I understood from the vignettes). If you want to set up for
> other people then the best way is probably to set up text files (or TinnR
> files) that have all the essential "start-up" commands on a "per chip"
> basis. This is pretty much the limit of my knowledge!
>
> Sherri
>
> On 19-Apr-10, at 7:30 PM, Christoph Knapp wrote:
>
>> That works well, thanks a lot, but how I said in a previous email, my
>> project is about writing an application which takes in many different
>> cel files without throwing exceptions. Its about making life easier
>> for people who know even less about that stuff than I do ;-). Thats
>> why I need a way to setup R so that it works without problems in a
>> standard way. Is there a possibility to retrieve information's from
>> the cel files itself what the latest version of annotation package is
>> it needs? Than I could just pass this information into the readAffy()
>> command similar to the way you suggested.
>>
>> Sorry for being a pain and thanks for the help.
>>
>> Christoph
>>
>> On 19 April 2010 23:28, Sherri Christian <sherri at mun.ca> wrote:
>>>
>>> sorry all, I forgot to change the name of the subject
>>> S
>>>
>>> Begin forwarded message:
>>>
>>> From: Sherri Christian <sherri at mun.ca>
>>> Date: April 19, 2010 8:53:25 AM NDT
>>> To: bioconductor at stat.math.ethz.ch, mkna005 at aucklanduni.ac.nz
>>> Cc: Sherri Christian <sherri at mun.ca>
>>> Subject: Re: Bioconductor Digest, Vol 86, Issue 19
>>> 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
>>>
>>>
>
>