[BioC] need help with SNP6.0 quantile normalization

[Benilton Carvalho]

additionally, the pd.* packages are not meant to be used with the
'affy' package, which is not designed for SNP chips.

b

On 12 October 2011 21:28, Vincent Carey <stvjc at channing.harvard.edu> wrote:
> 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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>
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