An apparatus, method, and computer program product are provided for determining a confidence measure for the output of a process for assessing proteomic and genomic information samples. Typically, data is received as the results from a microarry experiment. The confidence measure is intended to determine whether the results of the experiment have been degraded due to experimental error. Several criteria are used by which quality is determined. The criteria are preferably combined into a combined quality measure in order to account for several possible sources of error.