Good morning,
I wonder if anyone can answer this question: If I subset my Seurat object into celltype A and celltype B and then I merge it back together I see some differences in the counts@p. Why is this the case?
Please find below some pictures attached for illustration:
Before subsetting:
After subsetting into celltypes A (Macrophages) and Celltype B (all other cells):
Celltype A (Macrophages) :
Celltype B (all other cells):
Newly merged object:
The UMAP cluster seem to look as before however in slightly different positions.
However, comparing the counts I can see a difference:
Before:
After:
I had to re-run FindVariableFeatures, ScaleData, RunPCA, FindNeighbors, FindClusters and RunUMAP in the newly merged object since all reductions, commands were gone. However, I repeated the commands exactly in the way as before.
Any idea what is causing this difference? Thank you for any hint!
Ok I think I know what happened. The order of cells changed, otherwise its the same:
Could that be the explanation?