Body: <p>I am working with single cell data and using seurat to analyze the results. Often in manuscripts, we see the dotplots showing the expression of the marker genes or genes of interest across the different clusters. My question here is:</p>
  <p>When comparing expression of a gene (let's say geneA) across clusters, for example, let's say for cluster 0, the average expression for geneA that is plotted, is it calculated considering all the cells in the sample or all the cells in the cluster0? If it is calculating the average expression based on total number of cells present in cluster 0 (here), is it correct to compare the expression of geneA across all the clusters?
  Because among the different clusters, the number of cells are different, and the number of cells that are expressing geneA can vary a lot across the clusters.</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2021-08-11T01:27:20.247Z
Comments.Text: Hi, could you please add more context to your question? An example image of a Seurat dotplot that demonstrates your issues would help a lot here.
Comments.UserDisplayName: gringer
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2021-08-11T16:36:52.047Z
Comments.Text: Since it is showing mean expression among cells within a cluster, why would different number of cells across clusters worry you?
Comments.UserDisplayName: Phoenix Mu
Tags: <scrnaseq><seurat>
Title: Understanding the dot plot from seurat
ThreadText: # Understanding the dot plot from seurat
  
  (Asked by: username_0 on 2021-08-10)
  
  I am working with single cell data and using seurat to analyze the results. Often in manuscripts, we see the dotplots showing the expression of the marker genes or genes of interest across the different clusters. My question here is:
  
  When comparing expression of a gene (let's say geneA) across clusters, for example, let's say for cluster 0, the average expression for geneA that is plotted, is it calculated considering all the cells in the sample or all the cells in the cluster0? If it is calculating the average expression based on total number of cells present in cluster 0 (here), is it correct to compare the expression of geneA across all the clusters?
  Because among the different clusters, the number of cells are different, and the number of cells that are expressing geneA can vary a lot across the clusters.
  
  **Tags:** scrnaseq, seurat
  
  > **Comments:**
  > **username_1**: Hi, could you please add more context to your question? An example image of a Seurat dotplot that demonstrates your issues would help a lot here.  
  > **username_2**: Since it is showing mean expression among cells within a cluster, why would different number of cells across clusters worry you?  
  
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  ## 0 answers
  
  