# Estimate number of surrogate variables (Sv) n.sv <- num.sv(lcpm, mod, method="leek") print(paste("Estimated surrogate variables:", n.sv))

Now you run the core function to estimate the number of hidden batch effects.

library(DESeq2)

Once the download is complete and the executable is launched, follow these steps to process your first stack:

Below is a definitive guide to downloading and running Sequnator/SVA correctly.

SVA requires three primary inputs: