Lets say I have an adata object with 3 clusters.
Cluster1 has 100
Cluster2 has 10000
Cluster3 has 100
cells in it.
When I run
on the adata and I get the ranking for the cell specific markers.
The cell cluster size does not have an impact on the overall cell type specificity I assume?
Lets take the adata again from above:
This time I want to compare only cluster 1 and cluster 3 for different marker genes?
Would I do a subset of the adata to do that, or is there a way to specify that in the sc.tl.rank_genes_groups function?
Thank you & best wishes,