Batch correction for raw scRNAseq from multiple patients

[danyangli123]

Hi @akdess ,

I have several raw expression matrices from single-cell RNA-seq of different patients (potentially with batch effects). I’m following your GBM example, and when I checked the code for the CreateCasperObject function, I noticed that there’s no batch correction for raw data. I’m wondering if batch correction is needed in this case. Since CNV calling seems to be done separately for each patient (with BAF and expression signals combined separately for each), will any remaining batch effect impact the CNV results?

Thank you!

Best,
Danyang