<p>If both batches contain replicates of both groups (LT and C) then the presented code is what you should do, exactly pointed out in the vignette for the LRT: <a href="http://bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.html#likelihood-ratio-test" rel="nofollow noreferrer">http://bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.html#likelihood-ratio-test</a></p>

CC BY-SA 4.0
2023-01-24T10:14:01.697Z
Thank you. Please, what do you mean by "If both batches contain replicates of both groups (LT and C)" ? I know each sample is one independent person and we have sent samples to Qiagen in two times
Zizogolu
CC BY-SA 4.0
2023-01-24T21:24:24.653Z
It means exactly like it reads. Both batches need to contain replicates (preferably in comparable numbers) of both groups. Use `table(meta$batch, meta$group)` to see the distribution contingency table.
Ram RS
CC BY-SA 4.0
2023-01-23T19:37:53.713Z
2023-01-23T19:37:53.713Z
ATpoint
<p>I have sent two sets (two batches in matter of sending for sequencing) of different samples (plasma) to small RNA-seq to Qiagen company</p>
<p>This is how my meta data look</p>
<pre><code>&gt; head(meta)
           batch group    sex
30678.009 batch2     C   Male
30678.010 batch2     C Female
30941.001 batch1     C Female
30941.002 batch1     C   Male
30941.003 batch1     C   Male
30941.004 batch1     C   Male
&gt; tail(meta)
           batch group    sex
30941.016 batch1    LT Female
30941.017 batch1    LT   Male
30941.019 batch1    LT   Male
30941.022 batch1    LT Female
30941.023 batch1    LT   Male
30941.024 batch1    LT Female
&gt;   
</code></pre>
<p>I want to extract differentially expressed RNAs between my two groups without batch effect</p>
<p>I am doing this</p>
<p>Is this correct please?</p>
<pre><code>dds &lt;- DESeqDataSetFromMatrix(countData = count,
                              colData = meta,
                              design= ~ batch + group)

dds &lt;- DESeq(dds, test=&quot;LRT&quot;, reduced=~batch)

res &lt;- results(dds)
resultsNames(dds) 

[1] &quot;Intercept&quot;              &quot;batch_batch2_vs_batch1&quot; &quot;group_LT_vs_C&quot;         
&gt; 
</code></pre>

<r><deseq2><differential-expression><edger><batch-effects>
Batch correction in differential expression analysis
# Batch correction in differential expression analysis

(Asked by: username_0 on 2023-01-23)

I have sent two sets (two batches in matter of sending for sequencing) of different samples (plasma) to small RNA-seq to Qiagen company
This is how my meta data look
> head(meta)
           batch group    sex
30678.009 batch2     C   Male
30678.010 batch2     C Female
30941.001 batch1     C Female
30941.002 batch1     C   Male
30941.003 batch1     C   Male
30941.004 batch1     C   Male
> tail(meta)
           batch group    sex
30941.016 batch1    LT Female
30941.017 batch1    LT   Male
30941.019 batch1    LT   Male
30941.022 batch1    LT Female
30941.023 batch1    LT   Male
30941.024 batch1    LT Female
>   

I want to extract differentially expressed RNAs between my two groups without batch effect
I am doing this
Is this correct please?
dds <- DESeqDataSetFromMatrix(countData = count,
                              colData = meta,
                              design= ~ batch + group)

dds <- DESeq(dds, test="LRT", reduced=~batch)

res <- results(dds)
resultsNames(dds) 

[1] "Intercept"              "batch_batch2_vs_batch1" "group_LT_vs_C"         
>

**Tags:** r, deseq2, differential-expression, edger, batch-effects

---

## 1 answers

### Answer by username_1 on 2023-01-23. Score: 2

If both batches contain replicates of both groups (LT and C) then the presented code is what you should do, exactly pointed out in the vignette for the LRT: <http://bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.html#likelihood-ratio-test>

> **Comments:**
> **username_0**: Thank you. Please, what do you mean by "If both batches contain replicates of both groups (LT and C)" ? I know each sample is one independent person and we have sent samples to Qiagen in two times  
> **username_2**: It means exactly like it reads. Both batches need to contain replicates (preferably in comparable numbers) of both groups. Use `table(meta$batch, meta$group)` to see the distribution contingency table.  

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