SAINT-SPC-CTRL

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.