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.
removeBatchEffectattempts to remove batch effects, which is why you get data that may not make sense - removing batch effects is not an exact process, IMO. Rest assured, accounting for batch as a covariate wiil not have DESeq2 operating on batch-effect-removed data in the background. $\endgroup$