I was wondering how good the tool should work on a SMART-Seq 2 data set with "only" < 100 cells.
I'm getting the warning, that it might cause a problem. But my question is different.
I have run the
scDblFinder command on my
sce object after removing low qc cell identified via
addPerCellQCMetrics and only two cells were identified as doublet.
For some reason I needed to repeat the analysis and this time I have first ran the filtering for doublets only after removing low QC cells. This time though it identified 9 cells as doublets. I know it is not much, but it's still >10% in my data set.
I'm mainly interested in understanding if I can trust the results for such a small data set, and if so why there is such a big difference, depending how (or when) one run the search.