<p>I'm running FindAllMarkers</p>
<pre><code>markers &lt;- FindAllMarkers(scData_scTransform_PTX_only_res04_20PC_6000g_30mt_sb_removal_20210713_ann_exp0_counts, min.pct = 0.25, logfc.threshold = 0.25)
</code></pre>
<p>But was wondering if there is a function in seurat to get the raw (non-normalized) expression data from each cell type cluster</p>

CC BY-SA 4.0
2021-08-11T12:51:09.983Z
Hi, could you please add more context to this question so that we can understand why you want to find out this information? I've calculated *cell* counts per cluster, and visualised gene counts per cluster using scatter plots, but haven't yet run into a case where I'd need to work out *gene* count per cluster as a single statistic (whatever that means).
gringer
CC BY-SA 4.0
2021-08-20T08:45:12.517Z
@mmpp could it be that you meant to compare expression profiles of some genes (by means of a boxplot, for instance), to evaluate the differences between two conditions, in the same cell type, i.e. a cluster?
gbt
CC BY-SA 4.0
2021-09-15T21:58:44.257Z
are you trying to calculate pseudobulk average?
Code42
<r><gene><seurat><single-cell>
functions in seurat to calculate the gene count per cluster
# functions in seurat to calculate the gene count per cluster

(Asked by: username_0 on 2021-08-10)

I'm running FindAllMarkers
markers <- FindAllMarkers(scData_scTransform_PTX_only_res04_20PC_6000g_30mt_sb_removal_20210713_ann_exp0_counts, min.pct = 0.25, logfc.threshold = 0.25)

But was wondering if there is a function in seurat to get the raw (non-normalized) expression data from each cell type cluster

**Tags:** r, gene, seurat, single-cell
> **Comments:**
> **username_1**: Hi, could you please add more context to this question so that we can understand why you want to find out this information? I've calculated *cell* counts per cluster, and visualised gene counts per cluster using scatter plots, but haven't yet run into a case where I'd need to work out *gene* count per cluster as a single statistic (whatever that means).  
> **username_2**: @mmpp could it be that you meant to compare expression profiles of some genes (by means of a boxplot, for instance), to evaluate the differences between two conditions, in the same cell type, i.e. a cluster?  
> **username_3**: are you trying to calculate pseudobulk average?  

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## 0 answers

