Closed honghh2018 closed 3 years ago
Hi @All, Can anyone hear this question ?wait for the reply.
Hi @honghh2018
If I understand your question correctly, this issue might be your answer: https://github.com/satijalab/seurat/issues/2277
Best Katrin
Hi @ktrns ,
Sorry for the unclear description.
As my case, i want to remove the cell cycle influence for data integrated of clustering, so, should i run the CellCycleScoring function before samples integrated or after the data integrated. if i run before data integrated, it would be run CellCycleScoring for each sample and running integrated workflow to merge multiple samples into one subsequently, and then runing the CellCycleScoring .
Based above issue, which way should i take , when runing CellCycleScoring .
Best,
hanhuihong
Hi,
I would recommend cell cycle regression before integration on the individual samples. If you try the other route as well you can compare the scores and see if you see a significant difference.
Hi @SeuratLabs, I get a question , when runing the CellCycleScoring on the integrated sample. and i want to regress the impact of cell cycle genes. I wonder which running can be selected on integrated analysis. Whether or not I was runing the CellCycleScoring for each sample before data integrated or after the data integrated. The code showing below,
Runing the CellCycleScoring before integrated
x <- CellCycleScoring(x, s.features = s.genes, g2m.features = g2m.genes, set.ident = TRUE) x <- ScaleData(x, vars.to.regress = c("S.Score", "G2M.Score"), features = features) x <- RunPCA(x, features = features, verbose = FALSE) })
Runing the CellCycleScoring after integrated
Integrated <- IntegrateData(anchorset = anchors, dims = 1:30)
Now proceed with downstream analysis (i.e. visualization, clustering) on the integrated dataset. Commands are identical to the standard wor
kflow. Integrated<-CellCycleScoring(x, s.features = s.genes, g2m.features = g2m.genes, set.ident = TRUE) Integrated <- ScaleData(Integrated,vars.to.regress = c("S.Score", "G2M.Score") ) Just like the codes showing above, i cannot select the code with my integrated data analysis to remove the cell cycle impact without your help. Any advices would be appreciated. Best, hanhuihong