Answers.Body: <p>It's likely that the fold-change of the <code>topGene</code> is greater than 5. Consequently, the circle is being drawn and the text produced, but they're outside the bounds of the plot (the bounds don't update if you add a circle and text label). Look at the <code>log2FoldChange</code> column of <code>resLFC1[topGene, ]</code> and increase the bounds to encompass that.</p>
  
Answers.ContentLicense: CC BY-SA 3.0
Answers.CreationDate: 2018-04-13T21:07:54.417Z
Answers.LastActivityDate: 2018-04-13T21:07:54.417Z
Answers.UserDisplayName: Devon Ryan
Body: <p>I am trying to make <code>MA</code>-plot for my <code>bulk-RNA-seq</code> dataset and experiencing issues with it. I just copy-pasted the code that can be found here:</p>
  
  <p><a href="https://f1000research.com/articles/4-1070/v2" rel="noreferrer">https://f1000research.com/articles/4-1070/v2</a></p>
  
  <p>which is:</p>
  
  <pre><code>library("DESeq2")
  plotMA(resLFC1, ylim=c(-5,5))
  topGene &lt;- rownames(resLFC1)[which.min(resLFC1$padj)]
  with(resLFC1[topGene, ], {
    points(baseMean, log2FoldChange, col="dodgerblue", cex=2, lwd=2)
    text(baseMean, log2FoldChange, topGene, pos=2, col="dodgerblue")
  })
  </code></pre>
  
  <p>However, I am not getting the right plot with the top gene circled, but the following one:</p>
  
  <p><a href="https://i.sstatic.net/SwZ1R.png" rel="noreferrer"><img src="https://i.sstatic.net/SwZ1R.png" alt="enter image description here"></a></p>
  
  <p>Maybe it is a bug in the <code>plotMA</code> function, not sure. How can I reproduce the figure from the publication?</p>
  
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2018-04-13T10:23:50.460Z
Comments.Text: Are you sure that resLFC1 is created as stated in the article ? There seems to be a lot more points than in the article. Also, do you get any error or message?
Comments.UserDisplayName: llrs
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2018-04-13T15:22:08.697Z
Comments.Text: Are you sure the weird double quotes (“ versus ") are not the problem?
Comments.UserDisplayName: benn
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2018-04-13T18:39:12.480Z
Comments.Text: I corrected them, of course. `Rstudio` complains about it right away.
Comments.UserDisplayName: Nikita Vlasenko
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2018-04-14T17:44:50.447Z
Comments.Text: Your plot shows **all** genes as DE (red points). That’s suspicious.
Comments.UserDisplayName: Konrad Rudolph
Tags: <rna-seq><deseq2><figure-reproduction>
Title: plotMA function issue: can not circle genes
ThreadText: # plotMA function issue: can not circle genes
  
  (Asked by: username_0 on 2018-04-12)
  
  I am trying to make `MA`-plot for my `bulk-RNA-seq` dataset and experiencing issues with it. I just copy-pasted the code that can be found here:
  
  <https://f1000research.com/articles/4-1070/v2>
  
  which is:
  
  ```
  library("DESeq2")
  plotMA(resLFC1, ylim=c(-5,5))
  topGene <- rownames(resLFC1)[which.min(resLFC1$padj)]
  with(resLFC1[topGene, ], {
    points(baseMean, log2FoldChange, col="dodgerblue", cex=2, lwd=2)
    text(baseMean, log2FoldChange, topGene, pos=2, col="dodgerblue")
  })
  
  ```
  
  However, I am not getting the right plot with the top gene circled, but the following one:
  
  [![enter image description here](https://i.sstatic.net/SwZ1R.png)](https://i.sstatic.net/SwZ1R.png)
  
  Maybe it is a bug in the `plotMA` function, not sure. How can I reproduce the figure from the publication?
  
  **Tags:** rna-seq, deseq2, figure-reproduction
  
  > **Comments:**
  > **username_1**: Are you sure that resLFC1 is created as stated in the article ? There seems to be a lot more points than in the article. Also, do you get any error or message?  
  > **username_2**: Are you sure the weird double quotes (“ versus ") are not the problem?  
  > **username_0**: I corrected them, of course. `Rstudio` complains about it right away.  
  > **username_3**: Your plot shows **all** genes as DE (red points). That’s suspicious.  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_4 on 2018-04-13. Score: 4 | Accepted answer
  
  It's likely that the fold-change of the `topGene` is greater than 5. Consequently, the circle is being drawn and the text produced, but they're outside the bounds of the plot (the bounds don't update if you add a circle and text label). Look at the `log2FoldChange` column of `resLFC1[topGene, ]` and increase the bounds to encompass that.
  
  
  ---
  
  