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

CC BY-SA 4.0
2020-09-13T17:09:23.313Z
DESeq2 accounts for batch effect by treating it as a covariate when you use a formula that includes the batch variable. `removeBatchEffect` attempts 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.
Ram RS
<deseq2><limma><batch-effects>
Details of DESeq2 modeling a batch effect
# Details of DESeq2 modeling a batch effect

(Asked by: username_0 on 2020-09-13)

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.

**Tags:** deseq2, limma, batch-effects
> **Comments:**
> **username_1**: DESeq2 accounts for batch effect by treating it as a covariate when you use a formula that includes the batch variable. `removeBatchEffect` attempts 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.  

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