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t-sne interpretation #599

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robertzeibich opened this issue Jan 9, 2025 · 1 comment
Open

t-sne interpretation #599

robertzeibich opened this issue Jan 9, 2025 · 1 comment
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@robertzeibich
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robertzeibich commented Jan 9, 2025 •
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I ran pyscenic on the same dataset twice, but the input was filtered differently.

cellbender - mad filtering (based on https://www.sc-best-practices.org/preprocessing_visualization/quality_control.html)
aucell umap
pyscenic

qclus pipeline
aucell umap
image

aucell tsne
image

I still identify the same regulons, but in the 2nd run, regulons lighten up more.

These are epilepsy related TFs, claimed to be therapeutic targets (https://pmc.ncbi.nlm.nih.gov/articles/PMC9549512/).

What is more trustworthy now? Any suggestions for further investigations?
@robertzeibich robertzeibich added the question Further information is requested label Jan 9, 2025
@ruoyeruolan
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It seems that qclus pipeline removed much more cells than cellbender. How about the qc result of the raw expression matrix?

@robertzeibich robertzeibich changed the title tsne interpretation t-sne interpretation Jan 14, 2025
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@robertzeibich @ruoyeruolan