How does Prism compute the % of total variation in two-way ANOVA?
As part of two-way ANOVA, Prism reports the % of total variation accounted for by the interaction, the column factor and the row factor. These values are computed by dividing the sum-of-squares from the ANOVA table by the total sum-of-squares. The three values do not total 100% because Prism does not report the % of total variation accounted for by the residual (or error) part of the ANOVA table. If that were included too, the percentages would add to 100.
These values (% of total variation) are called standard omega squared by Sheskin (equations 27.51 - 27.53, and R2 by Maxwell and Delaney (page 295). Others call eta squared or the correlation ratio.
Prism simply reports how the total sum of squares is partitioned into the various components in your particular sample of data. Like R2 in linear regression, this simply is a description of your data and not a best-guess of a parameter in the population. It is possible to compute the best-guess for the population value. This is called omega squared (distinguish from the standard omega squared), but Prism does not compute it.