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.