One current approach to quality control in DNA array manufacturing is to synthesize a small set of test probes that detect variation in the manufacturing process. These fidelity probes consist of identical copies of the same probe, but they are deliberately manufactured using different steps of the manufacturing process. A known target is hybridized to these probes, and those hybridization results are indicative of the quality of the manufacturing process. It is not only desirable to detect variations, but also to analyze the variations that occur, indicating in what process step the manufacture changed. We describe a combinatorial approach which constructs a small set of fidelity probes that not only detect variations, but also point out the manufacturing step in which a variation has occurred. This algorithm is currently being used in mass-production of DNA arrays at Affyetrix.