SAINT-SPC-CTRL(1)					      General Commands Manual						 SAINT-SPC-CTRL(1)

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.

User Commands							    April 2012							 SAINT-SPC-CTRL(1)