During my work with single-cell RNA-seq data, I’ve often encountered confusion about PCA and specifically when to use the center and scale arguments in R’s prcomp() function. While tools like Seurat’s RunPCA() abstract away these details, understanding what happens under the hood is crucial for proper analysis and troubleshooting.
In this post, I’ll show you exactly what center and scale do, why they matter, and what happens when you get them wrong.