NAME

       saint-spc-ctrl - run SAINT with control data

SYNOPSIS

       saint-spc-ctrl   [interactionFile]   [preyFile]  [baitFile]  [nburnin]  [niter]  [lowMode]
       [minFold] [normalize]

DESCRIPTION

              nburnin = 2000: number of burn-in iterations in MCMC.

              niter = 10000: number of main iterations in MCMC.

              lowMode = 0/1 : exclude extremely high counts in the model.

              - If baits are densely connected or dataset is small (few baits), use 1.

              - otherwise, use 0.

              minFold = 0/1 : forcing separation between true and false distributions.

              - If user wishes to allow typical contaminants with significant

              differential enrichment over control purifications, use 0.

              - otherwise, use 1.

              normalize = 0/1 : divide the counts by the total spectral counts in each IP.

              nburnin = 2000: number of burn-in iterations in MCMC.

              niter = 10000: number of main iterations in MCMC.

              lowMode = 0/1 : exclude extremely high counts in the model.

              - If baits are densely connected or dataset is small (few baits), use 1.

              - otherwise, use 0.

              minFold = 0/1 : forcing separation between true and false distributions.

              - If user wishes to allow typical contaminants with significant

              differential enrichment over control purifications, use 0.

              - otherwise, use 1.

              normalize = 0/1 : divide the counts by the total spectral counts in each IP.

SEE ALSO

       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.