Hello, I used SVASeq to remove batch effects in my data set.
I have run SVASeq and gotten 8 surrogate variables and all of the covariates necessary for my conditions. How would I plot a more detailed PCA plot rather than the give plot svseq function that is used in the vignette? I am thinking of something more along the lines of RUVSeq's PCA plots. I also have the DESeq results of my data that was used to generate the SVASeq covariates.