Run saint scoring algorithm for protein-protein interaction data using label free quantitative proteomics data
saint-spc-noctrl [interactionFile] [preyFile] [baitFile] [nburnin] [niter] [fthres] [fgroup] [var] [normalize]
-burnin and iter: burn-in period and main iteration of MCMC
-fthres: frequency threshold above which probability is set to 0
-fgroup: frequency boundary dividing high and low frequency groups
-var: binary [0/1] indicator for modeling variance of the count data distributions
-normalize: whether to normalize the counts by total spectral counts
You can download a PDF file with more detailed instructions from
http://sourceforge.net/projects/saint-apms/files/
which is called saint-vignette-<YYYYMonDD>.pdf.