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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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Pseudo-bulk and perform QC #11

Closed lcolladotor closed 2 years ago

lcolladotor commented 3 years ago

Pseudo-bulk at the DLPFC layer (from #9) + pathology resolutions and check if we have enough spots. We can then do a PCA or MDS plot and some other QC.

Pathology resolution levels:

lcolladotor commented 3 years ago

We could also consider separating by WM vs grey matter if needed.

lcolladotor commented 3 years ago

Maybe drop more lowly expressed genes at the pseudo-bulk level?

lcolladotor commented 3 years ago

See filterByExpr() at https://bioconductor.org/books/release/OSCA/multi-sample-comparisons.html#differential-expression-between-conditions. This would be relevant if we subset to say Layer1, then do DE across pathology levels in just Layer1.

lcolladotor commented 3 years ago

Could be superficial vs deep GM using PCP4 as the boundary for superficial vs deep. Then it would be:

lcolladotor commented 3 years ago

Kristen @kmaynard12: there are no plaques on the WM. Good to know!