Hi,
I am trying to summarize and normalize Human Affymetrix data using the Bioconductor library "affy" and the "bg.correct" method, like I usually do with other datasets (recently done on Mouse data).
But I get this error about the cdf environment:

---
# Load libraries
>  library("affy")
>  library("affyPLM")
# List cel files
> list.celfiles()
# Read in cel files
> DataRaw <- ReadAffy()
> probes.bg.rma <- bg.correct(DataRaw, method = "rma")
Warning: unable to access index for repository http://brainarray.mbni.med.umich.edu/bioc/bin/macosx/universal/contrib/2.9
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
---


I found some discussions on this mailing list about this issue so I tried to fix it by installing the  "hugene10stv1.r3cdf" package.
But I got a warning and then still the same error when calling "bg.correct":

---
> source("http://bioconductor.org/biocLite.R")
> biocLite("hugene10stv1.r3cdf")
Using R version 2.9.2, biocinstall version 2.4.13.
Installing Bioconductor version 2.4 packages:
[1] "hugene10stv1.r3cdf"
Please wait...

Warning message:
In getDependencies(pkgs, dependencies, available, lib) :
  package ‘hugene10stv1.r3cdf’ is not available

>  probes.bg.rma <- bg.correct(DataRaw, method = "rma")
Warning: unable to access index for repository http://brainarray.mbni.med.umich.edu/bioc/bin/macosx/universal/contrib/2.9
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
---


I also tried to give the cdf filename to the "ReadAffy" function but still the same error :
---
> source("http://bioconductor.org/biocLite.R")
> biocLite("hugene10stv1.r3cdf")
#same warning
# Use ReadAffy with the CDF file name
> DataRaw<- ReadAffy(cdfname = "hugene10stv1.r3cdf")
> probes.bg.rma <- bg.correct(DataRaw, method = "rma")
Warning: unable to access index for repository http://brainarray.mbni.med.umich.edu/bioc/bin/macosx/universal/contrib/2.9
Error in getCdfInfo(object) : 
  Could not obtain CDF environment, problems encountered:
Specified environment does not contain hugene10stv1.r3cdf
Library - package hugene10stv1.r3cdf not installed
Bioconductor - hugene10stv1.r3cdf not available

# Try to get information about the cdf environment:
> getCdfInfo(DataRaw)
Warning: unable to access index for repository http://brainarray.mbni.med.umich.edu/bioc/bin/macosx/universal/contrib/2.9
Error in getCdfInfo(DataRaw) : 
  Could not obtain CDF environment, problems encountered:
Specified environment does not contain hugene10stv1.r3cdf
Library - package hugene10stv1.r3cdf not installed
Bioconductor - hugene10stv1.r3cdf not available
--- 


Please let me know what I possibly did wrong and how to fix this cdf environment issue.

Many thanks for your time and comprehension.
Best regards,

Roxane LEGAIE
Bioinformatician
--
Warwick Systems Biology Centre
Coventry House
University of Warwick
Coventry CV4 7AL
U.K.
+44 (0)24 761 50332
R.Legaie@warwick.ac.uk
http://www2.warwick.ac.uk/fac/sci/systemsbiology/

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