Hi,
Should variables with high values in loadings plot also have high correlation in the correlation circle in PLS-DA?
I noticed that based on the loadings plot the most important variable is (A_42_P582770), while in correlation circle the variable with the highest correlation is (A_43_P22469).
Can you please help me in explaining the plots?
hi @muna59,
the loadings are the actual variable coefficients in the component, whereas in the correlation circle plots the coordinates of the variable correspond to the correlation between the variable expression value and the component (on two components). I am not sure how you set up your cutoff threshold in the correlation circle plot, but that variable may have disappeared because its correlation to component 2 might be high…
Both outputs would often agree but they are showing/calculated differently.
You can read more about correlation circle plots here.
Kim-Anh
