Hi everyone, I have visualized some batch effects in my sequencing replicates and I have removed with the limma package as follows.
mat <- limma::removeBatchEffect(mat, vsd$batch)
After that, batch effect has been at least minimized and the PCA looks very good as I expected, however, at this point how can I proceed after this process? Can I use the normalized matrix for deseq? How can I perform the DE with the new matrix? is that possible? My deseq object looks like:
dds <- DESeqDataSetFromMatrix(countData = countData , colData = colData , design = ~ tissue + batch)