Each array was hybridized with RNA containing a single virus, except GSM40845, which was infected with both influenza A and respiratory syncytial virus. We assigned a correct result for each method if the top hit from the analysis was the same as the known infectious agent or, if that agent was not represented on the array, the top hit was a very closely related virus. In the case of GSM40845, we report a correct result if both viruses were at the top of the reported hits, to the exclusion of other virus species (but not closely related strains).