Answers.Body: <p>Your interpretation of <code>pct.1</code> and <code>pct.2</code> is misguided. If <code>pct.1 == 1</code>, the given gene was detected in all of the cells. This carries no information about high expression or low expression in the cell, just that it was detected. <code>avg_logFC</code> is the indication of expression <strong>levels</strong>. So your expectation, that </p>
  
  <blockquote>
    <p>"we would instead expect the genes to be expressed at high levels in the cells within the cluster but at low levels in cells not within the cluster"</p>
  </blockquote>
  
  <p>holds true, as indicated by the positive <code>avg_logFC</code> and significant p-values of the listed RP genes.</p>
  
  <p>Seurat use nautral log, so the FC of RPS6 in cluster 0 vs. all other clusters indicated is 2.718281828459^.55947=1.750.</p>
  
  <hr>
  
  <p>Seurat <code>FindMarkers()</code> <a href="https://www.rdocumentation.org/packages/Seurat/versions/3.1.2/topics/FindMarkers" rel="nofollow noreferrer">documentation</a>.</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-01-09T16:57:56.690Z
Answers.LastActivityDate: 2020-01-09T16:57:56.690Z
Answers.UserDisplayName: Kohl Kinning
Body: <p>I have generated a list of canonical markers for cluster 0 using the following command:</p>
  
  <pre><code>cluster0_canonical &lt;- FindMarkers(project, ident.1=0,  ident.2=c(1,2,3,4,5,6,7,8,9,10,11,12,13,14), grouping.var = "status", 
  min.pct = 0.25, print.bar = FALSE)
  </code></pre>
  
  <p>And I got the following output, but I do not understand why the canonically expressed <strong>ribosomal</strong> markers seem to be expressed at high levels in both the cells within the cluster AND cells that are NOT in the cluster (i.e. both pct.1 and pct.2 are close to 1, but P value is highly significant). We would not expect this for canonical markers - we would instead expect the genes to be expressed at high levels in the cells within the cluster but at low levels in cells not within the cluster. I don't seem to have such an issue with non-ribosomal genes within cluster 0 and cluster 0 is the only cluster where I get a high number of ribosomal genes as canonical markers.</p>
  
  <p><a href="https://i.sstatic.net/gtJs4.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/gtJs4.png" alt="enter image description here"></a></p>
  
Tags: <seurat>
Title: Seurat FindMarkers() output, percentage
ThreadText: # Seurat FindMarkers() output, percentage
  
  (Asked by: username_0 on 2020-01-09)
  
  I have generated a list of canonical markers for cluster 0 using the following command:
  
  ```
  cluster0_canonical <- FindMarkers(project, ident.1=0,  ident.2=c(1,2,3,4,5,6,7,8,9,10,11,12,13,14), grouping.var = "status", 
  min.pct = 0.25, print.bar = FALSE)
  
  ```
  
  And I got the following output, but I do not understand why the canonically expressed **ribosomal** markers seem to be expressed at high levels in both the cells within the cluster AND cells that are NOT in the cluster (i.e. both pct.1 and pct.2 are close to 1, but P value is highly significant). We would not expect this for canonical markers - we would instead expect the genes to be expressed at high levels in the cells within the cluster but at low levels in cells not within the cluster. I don't seem to have such an issue with non-ribosomal genes within cluster 0 and cluster 0 is the only cluster where I get a high number of ribosomal genes as canonical markers.
  
  [![enter image description here](https://i.sstatic.net/gtJs4.png)](https://i.sstatic.net/gtJs4.png)
  
  **Tags:** seurat
  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_1 on 2020-01-09. Score: 3 | Accepted answer
  
  Your interpretation of `pct.1` and `pct.2` is misguided. If `pct.1 == 1`, the given gene was detected in all of the cells. This carries no information about high expression or low expression in the cell, just that it was detected. `avg_logFC` is the indication of expression **levels**. So your expectation, that
  
  > "we would instead expect the genes to be expressed at high levels in the cells within the cluster but at low levels in cells not within the cluster"
  
  holds true, as indicated by the positive `avg_logFC` and significant p-values of the listed RP genes.
  
  Seurat use nautral log, so the FC of RPS6 in cluster 0 vs. all other clusters indicated is 2.718281828459^.55947=1.750.
  
  ---
  
  Seurat `FindMarkers()` [documentation](https://www.rdocumentation.org/packages/Seurat/versions/3.1.2/topics/FindMarkers).
  
  
  ---
  
  