malignant cells labeled in normal samples about luca HOT 2 CLOSED

Hi @rpeys,

there are two factors that likely play a role her:

• samples labelled as normal_adjacent might still contain a small number of tumor cells as the labelling by the pathologist might be imperfect
• the tumor cells were assigned based on unsupervised clustering. If you look at the UMAP of the epithelial cluster, you can see that there are no perfect boundaries between healthy and malignant cells, leading to some healthy cells being in the cluster that we assigned to tumor cells. This can be on the one hand a result of "over-integration" by scvi-tools, on the other hand it can be that some tumor are transcriptionally very similar to normal epithelial cells (and we would need information about their morphology and mutations to clearly separate them).

from luca.

Got it, thanks for shedding light!

from luca.