[BioC] need help with SNP6.0 quantile normalization

[Vincent Carey]

your R is too old.  please update to 2.13.2 and try again.

On Wed, Oct 12, 2011 at 4:25 PM, qian liu <qianliu9808 at yahoo.com> wrote:
> 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
>        [[alternative HTML version deleted]]
>
>
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