Answers.Body: <p>The expression values for each gene are scaled / standardized by subtracting the genes mean expression and dividing by its standard deviation. A value of -1 would imply it's one standard deviation below the mean expression for that gene.</p>
  
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Answers.CreationDate: 2018-10-28T05:54:06.930Z
Answers.Text: Hi, can I ask you another question about the findmarker function in Seurat(https://satijalab.org/seurat/pbmc3k_tutorial.html) ? Can you tell me it's that possible that the avg_logFC shows negative number? Is it the same explanation as the legend question's answer?
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Answers.CreationDate: 2018-10-28T20:24:36.960Z
Answers.Text: The average log fold change is something like `log(x) - log(y)` where x and y are the average expression of two different groups.  A negative log fold change would mean the average expression of the second group (y) is higher than the first (x)
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Answers.Text: Hi, thank you for your explanation. It really makes sense to me. And if the code'cluster1.markers <- FindMarkers(object = pbmc, ident.1 = 1, min.pct = 0.25)
  print(x = head(x = cluster1.markers, n = 5))' to find all markers of cluster1. Does it mean that x is cluster1 and y is the total cell?
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Body: <p><a href="https://i.sstatic.net/fXEYw.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/fXEYw.png" alt="enter image description here"></a></p>
  
  <p>Here is the code I used:</p>
  
  <pre><code>DotPlot(object = cluster, genes.plot = c("Hcn4","Shox2","Nkx2-5","Nppa","Tnnt2","Gja5","Tbx18","Tbx3","Isl1","Scn5a","Cacna1d"),  plot.legend=TRUE)
  </code></pre>
  
  <p>I was confused about the legend with the Negative number shown for <code>avg.exp.scale</code>. Does it mean that the cluster expressed the genes at low level or that gene was down regulated? (like the Shox2 in the "0" compared with "2").</p>
  
Tags: <r><seurat><single-cell>
Title: about dotplot legend meaning
ThreadText: # about dotplot legend meaning
  
  (Asked by: username_0 on 2018-10-23)
  
  [![enter image description here](https://i.sstatic.net/fXEYw.png)](https://i.sstatic.net/fXEYw.png)
  
  Here is the code I used:
  
  ```
  DotPlot(object = cluster, genes.plot = c("Hcn4","Shox2","Nkx2-5","Nppa","Tnnt2","Gja5","Tbx18","Tbx3","Isl1","Scn5a","Cacna1d"),  plot.legend=TRUE)
  
  ```
  
  I was confused about the legend with the Negative number shown for `avg.exp.scale`. Does it mean that the cluster expressed the genes at low level or that gene was down regulated? (like the Shox2 in the "0" compared with "2").
  
  **Tags:** r, seurat, single-cell
  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_1 on 2018-10-23. Score: 3 | Accepted answer
  
  The expression values for each gene are scaled / standardized by subtracting the genes mean expression and dividing by its standard deviation. A value of -1 would imply it's one standard deviation below the mean expression for that gene.
  
  > **Comments:**
  > **username_0**: Hi, can I ask you another question about the findmarker function in Seurat(https://satijalab.org/seurat/pbmc3k_tutorial.html) ? Can you tell me it's that possible that the avg_logFC shows negative number? Is it the same explanation as the legend question's answer?  
  > **username_1**: The average log fold change is something like `log(x) - log(y)` where x and y are the average expression of two different groups.  A negative log fold change would mean the average expression of the second group (y) is higher than the first (x)  
  > **username_0**: Hi, thank you for your explanation. It really makes sense to me. And if the code'cluster1.markers <- FindMarkers(object = pbmc, ident.1 = 1, min.pct = 0.25) print(x = head(x = cluster1.markers, n = 5))' to find all markers of cluster1. Does it mean that x is cluster1 and y is the total cell?  
  
  ---
  
  