I am running an sPLS-DA analysis on a metabolomics data set that I have tuned so that I have 3 components, with 7, 20, and 110 variables on each component, respectively.
I was using the “vip” function on my final sPLS-DA model to get variable importance projections, but find that I am getting non-zero values on variables on some of components for more variables than have been selected in the sPLS-DA (i.e., I get vip score for 7, 24 and 115 variables). But, when I extract the components from the same sPLS-DA model, it extracts the correct number of variables on each component (i.e., 7, 20, 110) that match the keepX values. So I am confident this isn’t an error with that input. Is this normal? I would have thought it wouldn’t be possible since the final sPLS-DA model limits the number of variables on each component. Perhaps I am just misunderstanding something.
Thank you so much for any help!