Remove the first PC?

[brianpenghe]

I saw that the tutorial uses the top 30 PCs for downstream analysis.
I was wondering whether it makes more sense to remove the first PC which is usually correlated to data quality.
Is there an easy way to check whether the first PC is correlated to quality?
Can we plot PC1's scores on UMAP etc. ?

[rcorces]

ArchR handles this automatically. see the corCutOff argument to various downstream functions.
https://www.archrproject.com/reference/addUMAP.html

[brianpenghe]

That's so smart :)