Number of cells in each clusters

Question

[singcell]

I wanted to determine if the number of particular cell type in a cluster is changing with the treatment conditions. I have used stimulated vs. control PBMC datasets vignette for this analysis comparing two conditions.

Question: I used the code below to get the counts in each cluster and treatment condition. I wanted to know if number of cells from the code below is normalized to the total number of cells sequenced for each samples.

table(Idents(immune.combined), immune.combined$stim)

Thank you.

Answer 1

[jared.andrews07]

No, that is just going to return counts of the idents (presumably clusters?) split by condition.

OSCA has a nice chapter on differential abundance testing, which is what it sounds like you're trying to do.

[singcell]

Thank you for your reply. Looks like with OOSCA I need to redo all analysis. Is there any way to get this info from Seurat or from any tool based on Seurat?

[jared.andrews07]

You can convert Seurat objects to the Bioconductor SingleCellExperiment class with the as.singlecellexperiment() function. I'd recommend giving that a try.