The present invention provides a simple, cost-effective, universal method for determining and/or quantifying differences in nucleic acid levels between two or more test mixtures without prior knowledge of the sequence of the nucleic acids of interest. The method involves providing a universal microarray containing a plurality of spots, where each spot contains a plurality, or pool, of different oligonucleotide probes having at least three distinct portions: a universal sequence portion, a short central variable "wobble" sequence portion, and a unique sequence portion. A set of probes is synthesized such that the universal sequence portion is the same for every probe, and all possible permutations of the wobble sequence and unique sequence portions are represented in approximately equal concentrations in the set. The probes are pooled on the universal microarray such that probes in a given spot have the same unique portion and every permutation of the short wobble, while probes on different spots have different unique portions. Primers complementary to the universal and wobble portions of the probes are used to synthesize, for example, cDNA from an mRNA preparation. The cDNA is hybridized to the universal microarray, and through the use of differential labeling, is identified and/or quantified.