Several questions related to normalization:
(1) I need to normalize the output?
(2) Are the outputs in proportions?
(3) Could I perform centered-log ratio transformation or additive-log ratio on the output?
You mentioned in the manuscript:
…quantile-transform the input features (species or gene family abundances) to the quantiles of a standard normal distribution in order to improve the detection power of the elastic net model.
(4) Could I perform the same normalization to the input features? This “sounds” like a good idea since the prediction model was trained on this type of normalization.