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I am wondering why the displayed delta value on the SAM graph (after running a SAM analysis) is different when you run different experiments. Does MeV "suggest" this delta value as the best one for your specific experiment or is it random and you should always set the delta value you consider best for your experiment ?
The starting delta value is not random, but it is defined in MeV as simply 1/4 of the maximum of the absolute values of observed scores (d). This is meant to be a starting point from which you adjust your delta to best fit your specific data.