Question about plotLoadings function in sPLS-DA

Hi all!

I am trying to figure out the meaning of this two plots:

Does this mean my model is better at discriminating categorie “1” from “0.5” than “0”?

Note that there are real hierarchy between the categories (1>0.5>0) although I know the model is not able to deal with this as I read in FAQ section.

My final model looks like this

Hi @David

Your interpretation is correct. As you can see in the sample plots, the first component is discriminating 1 from 0.5. if you strongly believe that the mentioned hierarchy is the true nature of the population structure, this outcome might simply be due to the relatively small sample size.

Hope it helps,