<p>I have an RNA-seq dataset and I am using <code>DEseq2</code> to find differentially expressed genes between the two groups.  I used pre-filtering to remove any genes that have no counts or only one count across the samples.
furthermore, I want to:</p>
<ul>
<li><p>remove genes in low counts by using a base mean threshold.</p>
</li>
<li><p>remove genes that have low counts compared to the rest of the genes.</p>
</li>
</ul>
<p><strong>Question</strong></p>
<p>Is there a common threshold used for the baseMean or a way to work out what this threshold should be?</p>

<r><rna-seq><deseq2><gene-expression>
baseMean threshold
# baseMean threshold

(Asked by: username_0 on 2022-04-27)

I have an RNA-seq dataset and I am using `DEseq2` to find differentially expressed genes between the two groups. I used pre-filtering to remove any genes that have no counts or only one count across the samples.
furthermore, I want to:

* remove genes in low counts by using a base mean threshold.
* remove genes that have low counts compared to the rest of the genes.

**Question**

Is there a common threshold used for the baseMean or a way to work out what this threshold should be?

**Tags:** r, rna-seq, deseq2, gene-expression

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## 0 answers

