<p>I am trying to access the normalized expression in both edgeR and DESeq2, yet the results are different. Does anyone know why?</p>
<p><strong>How to get normalized expression using edgeR:</strong></p>
<pre class="lang-r prettyprint-override"><code>
y &lt;- DGEList(...)
y &lt;- calcNormFactors(y, method = &quot;TMM&quot;)
v &lt;- voom(y, design, plot=FALSE)

# normalized expression
head(v$E)

</code></pre>
<p><strong>How to get normalized expression using DESeq2:</strong></p>
<pre class="lang-r prettyprint-override"><code>
dds &lt;- DESeqDataSetFromMatrix(...)
dds &lt;- estimateSizeFactors(dds)

# normalized expression
normalized_counts &lt;- counts(dds, normalized = TRUE)
head(normalized_counts)

</code></pre>
<p>Anyone know why the results are different? Aren't they both doing a version of log(cpm) under the hood? Or am I not comparing the right results from DESeq2?</p>

<rna-seq><deseq2><normalization><limma><edger>
What is the difference between Normalized Expression in EdgeR vs DESeq2?
# What is the difference between Normalized Expression in EdgeR vs DESeq2?

(Asked by: username_0 on 2022-04-29)

I am trying to access the normalized expression in both edgeR and DESeq2, yet the results are different. Does anyone know why?
How to get normalized expression using edgeR:

y <- DGEList(...)
y <- calcNormFactors(y, method = "TMM")
v <- voom(y, design, plot=FALSE)

# normalized expression
head(v$E)


How to get normalized expression using DESeq2:

dds <- DESeqDataSetFromMatrix(...)
dds <- estimateSizeFactors(dds)

# normalized expression
normalized_counts <- counts(dds, normalized = TRUE)
head(normalized_counts)


Anyone know why the results are different? Aren't they both doing a version of log(cpm) under the hood? Or am I not comparing the right results from DESeq2?

**Tags:** rna-seq, deseq2, normalization, limma, edger

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## 0 answers

