Let's say that I have one population that can be divided by a 2-level factor. I run MDS twice (using prcomp() {stats} in R), using the 2-level factor to separate my subjects.
If I reduce to two dimensions, I now have two plots. Let's say that on each of the MDS plots, I have 5 points (with the same labels). I can calculate a total of 10 (5x4/2) distances for plot 1, and 10 distances for plot 2.
Is it meaningful to quantitatively compare the distances of plot 1 and plot 2?