Does ScaleData of S.Score and G2M.Score will reduce the cell numbers for G1, S, G2M

Question

[alwayshope]

Dear experts,

May I have your guidance after removing the cell cycle effects by ScaleData(data, vars.to.regress = c("S.Score", "G2M.Score"), features = rownames(data)),

Will the cell numbers in the data object be reduced, or ScaleData only remove the cell proliferation marker genes effects, which do not reduce the cell numbers in the Seurat object(sample)?

Thank you very much!

Answer 1

[sp29]

No, it will not remove any cells from the Seurat object. You can verify it by looking at the object's dimensions (Just put the name of the Seurat object in the console).

(Not an ideal way) Or you can type View(your_seurat_object); this will open the object in the viewer where you can manually inspect.

[alwayshope]

Thanks a lot!

I checked and see the cell numbers of G1, S, and G2M after removing the cell cycles remain the same, so I am not sure if it really works, seems the removal is to remove some cell proliferation marker genes effects, not remove the proliferated cells.

Thank you very much for your guidance!