Provided by: saint_2.5.0+dfsg-3_amd64

**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.