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JonathanShor / DoubletDetection

Doublet detection in single-cell RNA-seq data.
https://doubletdetection.readthedocs.io/en/stable/
MIT License
87 stars 23 forks source link

NaN in doublets score #115

Closed hwlim closed 5 years ago

hwlim commented 5 years ago

Hi

I noticed that sometimes I get NaN from the following command:

doublets = clf.fit(raw_counts).predict(p_thresh=1e-7, voter_thresh=0.8)

Occasionally some elements in 'doublets' has NaN value, which nees some exception handling. Is it safe to ignore this NaN value cells as non-doublets?

Thank you.

adamgayoso commented 5 years ago

NaN are cells that are not confidently assigned either label. I would inspect their location relative to the called doublets and make a decision from there. However, the simplest thing to do may be to call them singlets.

hwlim commented 5 years ago

Thank you so much for the detailed advice!