Selection of HVG in scVI

[zvittorio]

Hi @PauBadiaM

often times the results from the integration are used for additional steps in an analysis. And for many tools, it is useful to use the full gene set, rather than the HVGs only.
As suggested here, if that is the goal one should run scVI on the full feature space

@Valentine_Svensson

The model can only work on the genes you have trained it on. If you want to do this I would suggest training the model on all genes. If you are exclusively using it for this normalization task, the slightly more ‘blurry’ representation you get is probably not an issue.

Is it sensible to apply HVG selection on scVI corrected (and normalized counts)?