The current literature establishes the importance of gene functional category and expression in promoting or suppressing duplicate gene loss after whole genome doubling in plants, a process known as fractionation. Inspired by studies that have reported gene expression to be the dominating factor in preventing duplicate gene loss, we analyzed the relative effect of functional category and expression. We use multivariate methods to study data sets on gene retention, function and expression in rosids and asterids to estimate effects and assess their interaction. Our results suggest that the effect on duplicate gene retention fractionation by functional category and expression are independent and have no statistical interaction. In plants, functional category is the more dominant factor in explaining duplicate gene loss.