How to get good clustering results?

[zznx]

Hi, Is this normal? If not, how can we optimize clustering?
DimPlot(merged_obj, cells.highlight = WhichCells(subset(merged_obj, SCT_snn_res.0.1=='T cells')))

Best
JianXiZhang

[samuel-marsh]

Hi,

Not member of dev team but hopefully can be helpful. There isn't really right answer about whether this is right here as it will depend on individual datasets. But given the scattering it would seem likely to me that you probably have some doublets in your data still. I would recommend checking all clusters and looking at canonical markers and evaluating whether further QC is needed. It is also possible that parameters for PCA, neighbors, clustering etc need to be adjusted.

I will move this to discussions section in case other members of community want to weigh in there.

Best,
Sam

[zznx]

Well,I have removed the double peaks with scDblFinder and I don't have a good idea, thanks for your reply

[samuel-marsh]

Doublet algorithms are not infallible. In fact they often they can often miss significant numbers of doublets.

[zznx]

Thank you. Any good suggestions?

[samuel-marsh]

I typically subset each individual cluster and recluster and analyze canonical markers.