Hi! I'm new to RNAseq analysis and had a few questions in regards to batch effects.

1) I have RNAseq data for two conditions obtained from two different batches that I am trying to analyse. I have included batch as a covariate while creating the DESeq object, but I am not sure if I am supposed to remove batch effects using limma, etc. before looking at differential gene expression or if accounting for it in the DEseq object is enough.

2) When doing a preprocessing analysis with PCA and batch removal, should the DEseq object not have ~batch as a covariate? I have currently included batch along with condition in the study design while creating the DESeq object, and then done a PCA with and without batch removal.