This invention pertains to methods for the analysis of biological data, particularly spectra, for example, nuclear magnetic resonance (NMR) and other types of spectra. More specifically, the present invention pertains to a method for processing a sample spectrum comprising: replacing each of one or more target regions in said sample spectrum with a corresponding replacement region of a master control spectrum to give a target-replaced sample spectrum, wherein said replacement region has been scaled so as to have the same fraction of the total integrated intensity in said target-replaced sample spectrum as it did in said master control spectrum. The present invention also pertains to analysis methods which employ the methods of the present invention, such as methods of identifying a biomarker or biomarker combination for an applied stimulus; classification of an applied stimulus; diagnosis of an applied stimulus; therapeutic monitoring of a subject undergoing therapy; evaluating drug therapy and/or drug efficacy; detecting toxic side-effects of drug; characterizing and/or identifying a drug in overdose.