[BioC] hugene10stv1cdf

[James W. MacDonald]

Hi Christoph,

Christoph Knapp wrote:
> Hi all,
> I'm trying for quite some time to get an analysis started. I keep
> getting this Error.

And I gave you the answer you need when you asked this on R-help last 
week (as did Martin Morgan)

https://stat.ethz.ch/pipermail/r-help/2010-April/235479.html

yet you continue to ask the same question. Did you try following the 
advice we gave you? If so, what were the results? If not, why not?

Best,

Jim


> 
> 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

-- 
James W. MacDonald, M.S.
Biostatistician
Douglas Lab
University of Michigan
Department of Human Genetics
5912 Buhl
1241 E. Catherine St.
Ann Arbor MI 48109-5618
734-615-7826
**********************************************************
Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues