When correcting my data for a batch effect using removeBatchEffect, some of the gene expression values become negative.
When searching for differentially expressed genes, I do not use the data above, but rather model the batch using deseq2 (design=~Batch + Condition).
However, I started worrying. When DESeq2 introduces a batch into the model, does it allow for negative values "behind the scenes"?
If it does, I do not understand how that can make sense, in the context of RNA-Seq data.