I have some questions about PCA in DeSeq2. Is the PCA based on all genes in the input list or the subset of highly differentially expressed genes? If so, how can I extract this subset? I have 5 groups in my PCA with multiple replicates and extracting the subset of genes that drive the PCA result will be very useful.
Also, is there a way to adjust the PCA image to make it more presentable?
Thanks a lot!