Replies: 1 comment
-
My suggestion would be to run PCA on the regressed out data before calling Scanorama, e.g., in Scanpy # Load adata, s_genes, and g2m_genes
sc.tl.score_genes_cell_cycle(adata, s_genes=s_genes, g2m_genes=g2m_genes)
sc.pp.regress_out(adata, ['S_score', 'G2M_score'])
sc.pp.scale(adata)
sc.tl.pca(adata)
sc.external.pp.scanorama_integrate(adata, 'batch', basis='X_pca') Then you can use |
Beta Was this translation helpful? Give feedback.
0 replies
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
-
Hi @brianhie , I tried to regress the cell-cycle genes effect before run scanorama. But I checked the source code of scanorama, it seemed that scanorama cannot use the result of regress out function for further analysis. How can I solve this problem?
Beta Was this translation helpful? Give feedback.
All reactions