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Why isn't it possible to run solo when there are categorical_covariate_keys? #3160

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alexlenail opened this issue Jan 22, 2025 · 0 comments

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@alexlenail
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I have a large experiment in which multiple mice were each separately sequenced in multiple 10X channels. So each mouse has multiple channels. I created by model with:

scvi.model.SCVI.setup_anndata(
    adata,
    batch_key='channel',
    categorical_covariate_keys=["Mouse"],
)

And now I want to remove doublets, but just found out

ValueError: Initializing a SOLO model from SCVI with registered categorical covariates is currently unsupported.

Should I leave out the "Mouse" covariate? I don't understand what I'm supposed to do here.

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