Dear all,
I have some trouble connecting snp 6.0 cdf file to cel file to perform quantile normalization (I do need do quantile normalization itself to extract reference distribution).  I think I already loaded the correct snp6 cdf file, but I still got the following error message saying "Specified environment does not contain pd.genomewidesnp.6". I am stucked at the first step of SNP6.0 analysis. Would you please give me some suggestion to solve the problem? Thank you very much.
 
Qian
 
 
library(pd.genomewidesnp.6)
RawData <- ReadAffy(celfile.path=getwd())
Step2 <- normalize.AffyBatch.quantiles(RawData)
Warning: unable to access index for repository http://brainarray.mbni.med.umich.edu/bioc/bin/windows64/contrib/2.11
Error in getCdfInfo(object) : 
  Could not obtain CDF environment, problems encountered:
Specified environment does not contain pd.genomewidesnp.6
Library - package pd.genomewidesnp.6cdf not installed
Bioconductor - pd.genomewidesnp.6cdf not available

> sessionInfo()
R version 2.11.1 (2010-05-31) 
x86_64-pc-mingw32 
locale:
[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252    LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C                           LC_TIME=English_United States.1252    
attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     
other attached packages:
 [1] makePlatformDesign_1.12.0 pd.genomewidesnp.6_1.0.0  makecdfenv_1.26.0         caret_4.67               
 [5] reshape_0.8.3             plyr_1.2.1                lattice_0.19-13           affy_1.26.1              
 [9] pdInfoBuilder_1.12.0      oligo_1.12.2              oligoClasses_1.10.0       affxparser_1.20.0        
[13] RSQLite_0.9-2             DBI_0.2-5                 Biobase_2.8.0            
loaded via a namespace (and not attached):
[1] affyio_1.16.0         Biostrings_2.16.9     grid_2.11.1           IRanges_1.6.17        preprocessCore_1.10.0
[6] splines_2.11.1        tools_2.11.1  
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