boxplot/histograms on preprocessed SNP affy data with crlmm package
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@javier-perez-florido-3121
Last seen 3.5 years ago
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
SNP oligo crlmm SNP oligo crlmm • 750 views
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@benilton-carvalho-1375
Last seen 18 months ago
Brazil/Campinas/UNICAMP
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 P?rez 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 > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor
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