I am analyzing a RNAseq dataset with a very obvious batch-effect using the DESeq2 (v1.4.5) R package. I account for the batch-effect in my model and in terms of differential expression it really improves the analysis. Now, I would like to visualize the data by principal component analysis and hierarchical clustering, which requires the adjusted values. However, I cannot figure out how to get the batch-corrected values. Thanks you for the help!