Compute differential expression between global proteins

[sgosline]

First copy this file to this repo. Then we can run the three tests on the protein data (syn25706561) and phospho data (syn25706631) ((@mdnestor can you please confirm that this is median centered but NOT stoichiometry corrected?)

We have three different experiments to compute: 1- healthy patient stroma vs treated patients 2- early (day 1 samples) vs late (all other treated samples) 3- each cell line vs. another (actually 3 comparisons)

Then repeat for phospho proteomics.

[CamiloPosso]

4) Early vs Late patient by patient basis