In an analysis of both new and old microarray data in the July Nature Genetics, Hughes et al. find that results are frequently skewed by aneuploidy (Nat. Gen. 2000, 25:333-337). Their first clue was an unexpected transcript profile similarity between two unrelated yeast mutants; the cause turned out to be an extra copy of an entire chromosome. Approximately 8% of the yeast mutants examined had chromosome-wide expression biases, even though most of these mutants are not known to have chromosome transmission defects. In five cases a gained chromosome had a close homologue of the deleted gene, and in two cases a growth advantage was demonstrated.