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Use median absolute deviations for filtering #53

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keller-mark opened this issue Jan 22, 2025 · 0 comments

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keller-mark commented Jan 22, 2025

Hi,
Thanks for the data products, they are very helpful.

It looks like for filtering, this is currently done using fixed thresholds

rna-data-products/bin/secondary_analysis.py

Line 64 in 41ab146

sc.pp.filter_cells(adata, min_genes=200)

I want to share that the current best practice is to use median absolute deviations https://www.sc-best-practices.org/preprocessing_visualization/quality_control.html#filtering-low-quality-cells

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