Dear Christoph,


What not do the data preprocessing step in Expression Consol software, then export the data with annotations as a text file, then import into R for further analysis.  

To import data into R, you can use read.delim or read.csv functions. 


Best regards,

Anthony


-----Original Message-----
From: bioconductor-bounces@stat.math.ethz.ch [mailto:bioconductor-bounces@stat.math.ethz.ch] On Behalf Of Christoph Knapp
Sent: Sunday, April 18, 2010 3:36 PM
To: bioconductor@stat.math.ethz.ch
Subject: [BioC] hugene10stv1cdf

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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