I have been mixOmics and I am really impressed with the analysis I can do. I am using sPLS and I have a question. I run perf first to select the optimal number of components using PLS. Then I run sPLS using the ncomp calculate from perf function and I also tuned the optimal number of keepX variables. After I run tune.spls I got outputs tune.spls.MAE $choice.keepX for optimal number of keepX
When I build the final sPLS model shall I use ncompspls or the ncomp from perf function?