[BioC] need help with SNP6.0 quantile normalization_How to extract reference distribution

[Benilton Carvalho]

You should describe what you want to do after you've got the normalized data.

SNPRMA already normalizes every sample to a fixed reference
distribution (obtained from HapMap). That means that you don't have to
do it yourself, as the package is already taking care of that for you.

If you need genotype calls, use the 'crlmm' package instead (the
method is called 'crlmm' as well).

If you must get the target distribution to do whatever you want, use:

pkg = 'pd.genomewidesnp.6'
fn = system.file('extdata', paste(pkg, 'Ref.rda', sep=''), package=pkg)
## this will load an object called 'reference'
load(fn)
head(reference)

b

On 12 October 2011 22:47, qian liu <qianliu9808 at yahoo.com> wrote:
>
> Thanks for the reply. I read the SNP 6.0 cel file using justSNPRMA in oligo
> package. After quantile normalization of this group of CEL files I want to
> extract the reference distribution, so that when I have a new sample I can
> normalize the new sample using the reference quantile normalized
> distribution. I don't want the new sample be part of the quantile
> normalization step.
> I found a function "normalize.AffyBatch.normalize2Reference", I am not sure
> if it will work on SNP array. I still don't know how to extract the
> reference quantile normalized distribution.  Please give me some suggestion.
>
> Thanks,
> Qian
> From: Benilton Carvalho <beniltoncarvalho at gmail.com>
> To: Vincent Carey <stvjc at channing.harvard.edu>
> Cc: qian liu <qianliu9808 at yahoo.com>; "bioconductor at r-project.org"
> <bioconductor at r-project.org>
> Sent: Wednesday, October 12, 2011 4:48 PM
> Subject: Re: [BioC] need help with SNP6.0 quantile normalization
>
> 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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>
>
>
> --
> Successful people ask better questions, and as a result, they get
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>
>
>



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Successful people ask better questions, and as a result, they get
better answers. (Tony Robbins)