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LieberInstitute / spatialDLPFC

spatialDLPFC project involving Visium (n = 30), Visium SPG (n = 4) and snRNA-seq (n = 19) samples
http://research.libd.org/spatialDLPFC/
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decide number of PCs we should use downstream #21

Closed abspangler13 closed 3 years ago

abspangler13 commented 3 years ago

find in OSCA the part where they talk about running PCAs. Make plots they suggest to check this. Check with Matt too to see what he did for his data.

https://github.com/LieberInstitute/spatialDLPFC/blob/main/code/analysis/01_build_SPE_all.R#L444

abspangler13 commented 3 years ago

run getClusteredPCs() with downsampled object

abspangler13 commented 3 years ago

decided to use 50 PCs or harmony dimensions