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ChuanXu1 avatar ChuanXu1 commented on June 16, 2024

@malonzm1, predicted_labels is not impacted, but majority_voting will be, due to the over-clustering step (different data structures will result in different clusterings).

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malonzm1 avatar malonzm1 commented on June 16, 2024

@ChuanXu1 Thanks. Would you say that if I were interested in majority_voting it would be better to perform celltypist before concatenation?

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ChuanXu1 avatar ChuanXu1 commented on June 16, 2024

@malonzm1, it depends. Usually, cells will be clustered in a better manifold when several datasets are combined and greater resolution is achieved, but sometimes clustering on a single dataset may reveal a better clustering shape (e.g., due to alleviated batch effect or optimal set of HVGs).

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