I am performing an RNA-seq analysis for differential gene expression and I have a question regarding the use of the package sva for the estimation of unknown batch effects.
In the sva vignette, it shows examples of using the package for estimation of surrogate variables and then performing DE analysis using the package limma (I am referring to the section 6 of the sva vignette: "Adjusting for surrogate variables using the limma package")
Is that possible to do the same using the package edgeR instead of limma?
Or is sva not compatible with edgeR?
Sorry if this is a dumb question. I am a little new to the bioinformatics world.