I was wondering if scVI’s differential expression module still works in the following case:
I integrated two datasets with scANVI:
- dataset1: healthy lung tissue, mixture of immune, stromal, endothelial and epithelial cells, 10x
- dataset2: lung cancer tissue, also a mixture of the same cell types, Smart-seq2
Judging from the UMAP plot, the integration worked reasonably well.
I would like to compare for each cell type healthy vs. tumor samples.
With any classical DE method (i.e. a linear model), I’d expect the results of this comparison
to mainly reflect the technical differences between the 10x and the Smart-seq2 platforms. Since scANVI appears to successfully reduce the batch effects in the latent representation, I was wondering if such comparisons between datasets from different platforms become feasible as well.