Why are some cells of Cell type A located in Cell type B in scRNA-seq clustering?
Hi all,
I have a question about the scRNA-seq clustering. In my data or some paper, although Cell type A and B are different cell types and are located far away in UMAP, some cells of Cell type A located in Cell type B. Take my UMAP as an example, Astro4 (green) clusterd well with other Astrocyte cluster, but some cells of Astro4 located in Microglia clusters (topright).
I think this is caused by a doublet issue or low capture efficiency or something...but I'm not sure...
How best to explain this phenomenon?
Thank you,
Joonhong
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Clustering is commonly done on the principal components while UMAP is a different algorithm, so some discrepancy is not unexpected. It would also depend on what the colors are based on, is this clusters as in the graph-based clustering, or something else? HArd to comment without details.
I performed the analysis by following the seurat integration tutorial. This method is graph-based clustering.
That figure show only astrocyte clusters among all brain cells using subset function.
https://satijalab.org/seurat/articles/integration_introduction.html
Thank you.