Christopher provided some great feedback on your pipeline so I’ll just encourage you to check out our updated vignette which expands on all the available methods and their functionalities mixOmics vignette.
I will check the updated vignette once again.
I think “signature metabolites” or “selected metabolites” would be a better term to describe the selected features.
Thanks for your suggestion!
Also, can you help me answer my question regarding further statistical analysis on detected signature metabolites?
The most “significant” metabolites refer to those which could actually differentiate among the groups, and also the targeted metabolites we want to filter. We set the VIP score greater than 1 and AUC greater than 0.7. After filtering, we did some further logistic regression analysis to confirm their effects on group differentiation again.