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


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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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