Is it normal if regress out the cell cycle effects but the DEGs are quite the similar (no big changes)

Question

[alwayshope]

Dear experts,

Is it normal after regressing out the cell cycle effects but the DEGs are quite similar (no big changes)?

The scRNAseq data are from one cell type, less than 50% of cells show detected expression of Ki67, when using the Seurat to regress out the cell cycle effects, the down stream analysis using the same parameters that without regressing out the cell cycle effects nearly have no changes on the DEGs for treat vs control for each cell cluster.

Thank you very much!

[fracarb8]

Scaling is mainly affecting the PCA and clustering of your data. DE analysis is usually run on the uncorrected counts (e.g. data slot). If you want to account for the cell cycle effect, you can either set slot = scale.data, specify the confounders during test (e.g. test.use = "MAST", latent.vars = ..., or run DE on the different phases (e.g. id1 = "S", id2= G1)

[alwayshope]

This helps a lot! Thank you very much!