Relative noise is a single scalar value that is used to predict the maximum value of the expected noise at any point and is calculated from the measured signal and a mathematical noise model. The mathematical noise model is selected or estimated from an observation that includes statistical and/or numerical modeling based on a population of measurement points. An absolute noise for a plurality of points of the measured signal is estimated. An array of values is calculated by dividing each of a plurality of points of the absolute noise by a corresponding expected noise value calculated from the mathematical noise model. The relative noise is calculated by taking a standard deviation of a plurality of points of the array. The relative noise can be used to calculate scaled background signal noise, filter regions, denoise data, detect false positives from features, calculate S/N, and determine a stop condition for acquiring data.