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LieberInstitute / Visium_SPG_AD

Visium SPG AD project (n = 10) using Visium Spatial Proteogenomics (Visium-SPG) on dissections from the inferior temporal cortex (ITC) from Alzheimer's disease cases and controls.
https://research.libd.org/Visium_SPG_AD
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Choose dynamic thresholds for pathologies #26

Closed sparthib closed 2 years ago

sparthib commented 2 years ago

Based on Br_3874 in https://github.com/LieberInstitute/Visium_IF_AD/tree/master/plots/07_spot_qc/outliers

NpTau = max(NpTau of 004 and 106) same with PpTau NAbeta = max(Q2 for all controls) or max(Q3 for all controls)

Screen Shot 2022-02-15 at 8 20 44 PM Screen Shot 2022-02-15 at 8 29 02 PM
lcolladotor commented 2 years ago

I think that we could also use dynamic thresholds for PpTau and PAbeta (same formulas as for n).

Then we might consider a spot to have pTau pathology in #25 if it's either an outlier on PpTau or NpTau (similar for Abeta).