[BioC] boxplot/histograms on preprocessed SNP affy data with crlmm package

[Benilton Carvalho]

Probably

http://www.jstatsoft.org/v40/i12/paper

is relevant for what you want to achieve?

Also, the accessors calls(), confs() should work to get the results
you want... SNR is stored in the phenoData slot, so SNPSetObject$SNR
should get you what you need (check head(pData(SNPSetObject)) )... for
feature information, check head(fData(SNPSetObject)) .

b

On 20 June 2012 12:20, Javier Pérez Florido <jpflorido at gmail.com> wrote:
> Dear list,
> I have an SNP 6.0 affymetrix data set and before genotype calling, an
> exploratory analysis (boxplot, histograms, MAplots) on raw data are run by
> means of the oligo package.
>
> However, I would like to run such exploratory analysis once the data is
> normalized. crlmm function from crlmm package performs genotype calling and
> returns an SNPSet object (calls, confs, SNP quality score and SNR
> information). However, I don't know how to access to normalized data to run
> such exploratory analysis and compare such analysis with the one run with
> raw data.
>
> Any suggestions?
> All the best,
> Javier
>
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