Leiden clustering gives me different results when I run it

Help scanpy
1

Hello,

I am analyzing some data using scanpy. I am following the following steps: QC, PCA, harmony integration, UMAP, leiden clustering, and finding the markers.
However, every time I run the whole notebook I get different amount of clusters for the same resolution at leiden clustering. How can I make sure that I get consistent results? The clusters do look similar.
Could the problem be at the harmony or leiden step?

Thank you

2

Hello! In my experience this was caused by the harmony results (Results not reproducible · Issue #24 · slowkow/harmonypy · GitHub). If I used the same harmony embeddings from a prior run, I obtained visually identical leiden and umap results. Hope that helps!