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Issue on page /preprocessing_visualization/quality_control.html #306

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jffpviana opened this issue Nov 12, 2024 · 0 comments
Open

Issue on page /preprocessing_visualization/quality_control.html #306

jffpviana opened this issue Nov 12, 2024 · 0 comments

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@jffpviana
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jffpviana commented Nov 12, 2024

Hello! Thank you for developing this resource, it's much appreciated.
My question is regarding the outlier filtering, more specifically the expression:

adata.obs["outlier"] = (
    is_outlier(adata, "log1p_total_counts", 5)
    | is_outlier(adata, "log1p_n_genes_by_counts", 5)
    | is_outlier(adata, "pct_counts_in_top_20_genes", 5)
)
adata.obs.outlier.value_counts()

I tried to replicate this but each statement just overwrites the first one. In the end no cells are removed, no matter what threshold I use. Am I doing something wrong or is this a mistake?

Thank you in advance!

EDIT: Apologies, this was a problem with my modification of the code and it's now working! Please close the issue.

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