1. A method for processing data, the method being implemented in a computer, the method comprising the steps of: selecting a metric for determining substantially optimal combination of true positives and false positives differentials between pairs of elements in at least one data set; applying an optimization technique by means of a computer usable medium having computer readable code being capable of causing a computer system to apply the optimization technique; and obtaining, from the results of the optimization technique, a value for at least one optimization parameter, said value for at least one optimization parameter resulting in substantially optimal combination of true positives and false positives; wherein a number of true positives and false positives are a function of the at least one optimization parameter; whereby the data sets include data obtained from large-scale measurements of organismal and cellular state involving multiple independent measurements of each parameter, said parameters including genes, transcripts and proteins; wherein the substantially optimal combination of true positives and false positives differentials in the data set utilized for decision making to increase confidence on the use of the data in activities including manufacturing, handling, hybridization, and gene expression.