Batch Effect: To Correct or Not for Bulk RNA-seq Data

A colleague sent me a PCA plot last week. Three replicates per condition, control vs KO of a gene. PC1 cleanly separated replicate 1 from replicate 2 from replicate 3. PC2 separated control vs KO. The question that followed: should we run limma::removeBatchEffect() before differential expression? The answer is &ldquo;it depends,&rdquo; and most of the time the answer is &ldquo;no, do not…