Cell cycle regression and n_embedding tuning

Hello Constantin,

I've been playing a bit with lemur on the following dataset. Basically, a cell line treated under multiple conditions (~10) and I have two replicates of the experiment. However, the cell cycle is a clear confounding factor. How should I regress it? Is the next way the correct one to follow?
`fit <- lemur(sce, design = ~ conditions + experiment, n_embedding = 15, test_fraction = 0.25)`
`fit <- align_harmony(fit, design = ~ Phase)`

I've already tried this and the cell cycle effect disappears, but I don't know if this is technically a good procedure. On the other hand, `fit <- align_by_grouping(fit, grouping = sce$Phase)` does almost nothing. What would be your way to proceed?

Also, would you mind to share some ideas on how to tune the n_embedding? I've read that it follows the same logic as PCs, but maybe you've found a normal range of use (e.g. 15-20) or you put it larger for very heterogeneous data.

Thanks a lot!

Pedro