<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>

CC BY-SA 4.0
2019-02-28T14:41:55.663Z
2019-02-28T14:41:55.663Z
TimStuart
<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.sstatic.net/FYhqE.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/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>

<seurat><single-cell>
Why does my SplitDotPlotGG plot show differential expression of a gene but Seurat::FindMarkers() function does not return it?
# Why does my SplitDotPlotGG plot show differential expression of a gene but Seurat::FindMarkers() function does not return it?

(Asked by: username_0 on 2019-02-28)

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.

**Tags:** seurat, single-cell

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## 1 answers

### Answer by username_1 on 2019-02-28. Score: 2 | Accepted answer

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.


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