[BioC] EdgeR for proteomics data

Ryan rct at thompsonclan.org
Tue Jan 14 17:38:29 CET 2014


As mentoined in the help text for calcNormFactors, the TMM 
normalization method is described in the paper "A scaling normalization 
method for differential expression analysis of RNA-seq data" by 
Robinson & Oshlack. The best way to familiarize yourself with this 
method would be to read the paper: 

For what it's worth, one of my colleagues used edgeR on some proteomic 
data and decided that the default normalization strategy was not 
suitable for his data. I don't remember exactly what he ended up using 

-Ryan Thompson

On Mon Jan 13 17:32:36 2014, Phinney, Brett wrote:
> Hi everyone, I have been experimenting with using EdgeR with proteomics data (spectral counts for now). I was a little confused how the TMM normalization works on proteomics data. I  basically just read in my spectral counting data  as a data matrix
> And then
> normFactors <- calcNormFactors(counts)
> but I'm not sure exactly how it is calculating the normalization factors?
> Any help would be greatly appreciated
> Cheers
> Brett
> ---
> Brett S. Phinney, Ph D.
> UC Davis Genome Center
> www.proteomics.ucdavis.edu<http://www.proteomics.ucdavis.edu>
> cell = 530-771-7055
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