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theislab / scarches

Reference mapping for single-cell genomics
https://docs.scarches.org/en/latest/
BSD 3-Clause "New" or "Revised" License
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Multiple categorical_covariate_keys not allowed #208

Open Yuki-YqHuang opened 11 months ago

Yuki-YqHuang commented 11 months ago

Hi,

I'm using scANVI-scArches to integrate data from several studies. Each study has several samples. So I set up the model with categorical_covariate_keys=["sample", "study"]. This worked when integrating the data. However, when I was trying to project new data to the reference data. I got an error saying scArches currently does not support multiple categorical_covariate_keys. Given this situation, is it reasonable only including batch_key="sample", ignoring the differences between studies? I also noticed that HLCA atlas was also built from several studies with multiple samples. How did you deal with this situation?

Thanks, Yuqi

Koncopd commented 11 months ago

Hi, @Yuki-YqHuang , you can, for example, concatenate sample and study.