SingleR for integrated scRNA-seq analysis

1

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 : 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.


scRNA-seq


singler


integrated


Assay

• 1.1k views

The assay should be RNA, since SingleR expects expression values.


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