text: user3968: I have analysed  and clustered my single cell rna seq data with methods in the Seurat package. After clustering, I obtained two main clusters: 0 and 1. I used the Seurat SplitDotPlotGG function to visualise the differential expression of a gene of interest X. 
  SplitDotPlotGG(object,
                 grouping.var = "clusterID", 
                 genes.plot = c("geneX"),
                 cols.use = c("blue", "red"), plot.legend = T) 
  
  
  The plot shows clearly that there could be a significant differential expression of geneX between the conditions represented in clusters 0 and 1. However, I cannot see geneX in the list of differentially expressed genes returned when I run:
  FindMarkers(object, ident.1 = 0, ident.2 = 1, genes.use = "geneX")
  
  Is there be any explanation for this?
  Thanks in advance.
  
  user3415: You're showing groups 1 and 2 in the plot but comparing groups 0 and 1 in the differential expression test, so you need to instead set ident.1 = 1, ident.2 = 2 in FindMarkers.
  The FindMarkers function by default only returns genes with >0.25 log fold-change expression, with >3 cells in each group. It's possible that these criteria are not being met for gene X. You can try changing these defaults, setting logfc.threshold = 0 to return all genes.
  
original_text: 3968: <p>I have analysed  and clustered my single cell rna seq data with methods in the Seurat package. After clustering, I obtained two main clusters: 0 and 1. I used the Seurat <strong>SplitDotPlotGG</strong> function to visualise the differential expression of a gene of interest X. </p>
  
  <pre><code>SplitDotPlotGG(object,
                 grouping.var = "clusterID", 
                 genes.plot = c("geneX"),
                 cols.use = c("blue", "red"), plot.legend = T) 
  </code></pre>
  
  <p><a href="https://i.stack.imgur.com/FYhqE.png" rel="nofollow noreferrer"><img src="https://i.stack.imgur.com/FYhqE.png" alt="Expression of geneX"></a></p>
  
  <p>The plot shows clearly that there could be a significant differential expression of geneX between the conditions represented in clusters 0 and 1. However, I cannot see geneX in the list of differentially expressed genes returned when I run:</p>
  
  <pre><code>FindMarkers(object, ident.1 = 0, ident.2 = 1, genes.use = "geneX")
  </code></pre>
  
  <p>Is there be any explanation for this?
  Thanks in advance.</p>
   3415: <p>You're showing groups 1 and 2 in the plot but comparing groups 0 and 1 in the differential expression test, so you need to instead set <code>ident.1 = 1, ident.2 = 2</code> in <code>FindMarkers</code>.</p>
  
  <p>The <code>FindMarkers</code> function by default only returns genes with >0.25 log fold-change expression, with >3 cells in each group. It's possible that these criteria are not being met for gene X. You can try changing these defaults, setting <code>logfc.threshold = 0</code> to return all genes.</p>
  