Hi, I have data from a specific cell from mouse fed with a certain diet. I integrated 4 datasets that were measured at four different time for the integrated single-cell RNA seq analysis. I have been referring to the Seurat vignette : https://satijalab.org/seurat/v3.1/immune_alignment.html.
I am using SingleR to identify cell type for each cluster and I am wondering if I need to set
DefaultAssay as "RNA" or "integrated". I tried both, but they gave me slightly different results for cell type identification.
Should I keep
DefaultAssay as "RNA" or "integrated"?
Any thoughts and advice are greatly appreciated. Thank you.