Abstract: The invention relates to a method of preparing clusters of reference hybridization patterns for a sample nucleic acid, comprising providing an array comprising a plurality of nucleic acid molecules, wherein said plurality of nucleic acid molecules is derived from at least two different sources, providing at least two different reference hybridization patterns by hybridizing said array with at least two different reference nucleic acids, wherein the sources of said at least two different reference nucleic acids are separable into at least two groups on the basis of a value for at least one phenotypic parameter, and clustering the reference hybridization patterns by unsupervised multivariate analysis.