Hi!
I am trying to reproduce Hail’s pc_project output using plink –score. I am adding the variance-standardize option and keeping mean imputation. Plink notes that “PCs will be scaled a bit differently from ref_data.eigenvec; you need to multiply or divide the PCs by a multiple of sqrt(eigenvalue) to put them on the same scale”, how does Hail scale the PCs? is there a specific scaling equation that I can use to make my plink output similar to Hail’s?
Thank you