[BioC] need help with SNP6.0 quantile normalization
Vincent Carey
stvjc at channing.harvard.edu
Wed Oct 12 22:28:21 CEST 2011
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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