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[Bug] >99% cells annotated as NaN #4

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pakiessling opened this issue Sep 20, 2024 · 0 comments

pakiessling commented Sep 20, 2024 •

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Hi Quentin,

I just tried Novae out on my heart cohort. 46 samples ~ 2 million cells.
I used novae-human-0 with both zero_shot and fine_tune .

I used counts and let Novae handle the preprocessing

Both times almost all cells were annotated as NaN:

adata.obs["novae_domains_7"].value_counts(normalize=False,dropna=False)
novae_domains_7
NaN      1997204
D1015      12403
D1016       1755
D1012        827
D966         266
D1008        164
D993         102
D282           2

Do you know what could cause this?

Novae 0.1.0

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