1. An apparatus for determining a confidence measure for the output of a process for assessing proteomic and genomic data samples, with the output represented as a set of signals, the system comprising: a memory for storing digital data, in the form of data points representing data samples, generated from at least a portion of the signals in the set of signals; a processor coupled with the memory for accessing the digital data therefrom, and for determining a confidence measure for each of at least a portion of the signals for which digital data is stored in the memory; the confidence measure being indicative of a confidence level in the quality of the output of the process for assessing proteomic and genomic data samples; and wherein each data point has a perimeter, wherein each data point is contained in an image snip having borders, and wherein the confidence measure is an open perimeter confidence measure for the data point, determined based on the percentage of the perimeter of a data point occupied by the border of its respective snip.