I have 4 different single-cell RNAseq experiments, each one representing a different sample of cell type population. I'd like to merge them to a single dataset. However, different cell types are enriched in each sample, and different samples can represent also different conditions (control and disease).
If I run a PCA on the merged dataset (without any processing of data) I find that the different sample's cells cluster separately. This could be due to biological and technical (i.e. batch effects) variation.
Is it possible to merge these different samples while retaining a good amount of information or should they be analyzed separately?