Figure 2

Evaluation of normalization and similarity metric parameters. A training set of 32 microarrays was used to evaluate all nonequivalent combinations of intensity and energy vector normalization (N, none; Q, quadratic; S, sum; U, unit-vector) and similarity metric (DP, dot product; ED, similarity based on Euclidean distance; PC, Pearson correlation; SR, Spearman rank correlation; UP, uncentered Pearson correlation) parameters. For each combination of parameters, intrafamily and interfamily separations were calculated for each microarray as the score of the virus profile matching the virus present in the sample minus the score of the best scoring nonmatch profile from the same or a different virus family (top and bottom panels, respectively), normalized by the range of all scores on that microarray. Bars represent the mean, and error bars represent the standard deviation (±) of separation values from all microarrays. The best performing combinations are shown in order of increasing performance (calculated as the product of the intrafamily and interfamily separation means divided by the corresponding standard deviations).