The output of scANVI

Hi,
Thank for the wonderful libraries.
I have some questions. After doing integration, should I get model_scanvi.get_latent_represention() or model_scanvi.get_normalized_expression() as a new X matrix to do downstream analysis such as DGE or GSEA? When I plotted the UMAP of get_normalized_expression() method, the result is not really integrated in the right way.


The output matrix of get_latent_representation() has negative values. If we should take this matrix as X of annotated data, how can we avoid these negative values (by setting some parameters of scANVI or scVI)
Thank you so much for helping me!