I am trying to perform a multilevel analysis but with Pareto scaling. Since this is not an option in MixOmics, I have been doing it before calculating the model. Even though this works (perf results are not different), I am trying to do a multilevel analysis, which would require me to calculate the within variation dataset before scaling (using the withinVariation function). However, the perf function yields very different results in this case. Why could this be and how can it be fixed?
Thanks in advance for your response,