Figure 3.

When collapsing genes to modules, the optimal method depends on the goal of the analysis. A-C) Across several studies in human brain (A), mouse brain (B), and human blood (C) the MaxMean parameter generally produces better ranked expression correlations (left column) when setting the connectivityBasedCollapsing parameter to FALSE. On the other hand, better connectivity correlations (right column) are found when setting connectivityBasedCollapsing to TRUE, in some cases producing higher correlations that even the module eigengene (5.ME). Labelling as in Figure 2 B-D.