<p>I have a spreadsheet of CPM values</p>
<p>I want to visualize the top 20 genes expressed across my samples</p>
<p>This is how my data look like</p>
<pre><code>&gt; head(b[1:5,1:5])
                 30566-001 - CPM 30566-002 - CPM 30566-003 - CPM 30566-004 - CPM 30566-005 - CPM
hsa-miR-548ap-3p               0               0               0               0               0
hsa-miR-548t-3p                0               0               0               0               0
hsa-miR-548e-3p                0               0               0               0               0
hsa-miR-548az-3p               0               0               0               0               0
hsa-miR-548f-3p                0               0               0               0               0
&gt; dim(b)
[1] 2632   42
&gt; 
</code></pre>
<p>How I can do that?</p>

CC BY-SA 4.0
2021-11-25T15:03:58.490Z
Just make a heatmap?
user438383
CC BY-SA 4.0
2021-11-25T15:07:41.110Z
Then from a data frame with 2632 genes, how I select a list of genes for heatmap? Because a heatmap with 2632 genes is not clear while my main purpose is to shows a list of highly expressed genes across my samples
Zizogolu
CC BY-SA 4.0
2021-11-25T15:14:53.153Z
select the N genes with the highest average expression across all samples?
user438383
<r><differential-expression><deseq2>
Visualizing top expressed genes
# Visualizing top expressed genes

(Asked by: username_0 on 2021-11-25)

I have a spreadsheet of CPM values
I want to visualize the top 20 genes expressed across my samples
This is how my data look like
> head(b[1:5,1:5])
                 30566-001 - CPM 30566-002 - CPM 30566-003 - CPM 30566-004 - CPM 30566-005 - CPM
hsa-miR-548ap-3p               0               0               0               0               0
hsa-miR-548t-3p                0               0               0               0               0
hsa-miR-548e-3p                0               0               0               0               0
hsa-miR-548az-3p               0               0               0               0               0
hsa-miR-548f-3p                0               0               0               0               0
> dim(b)
[1] 2632   42
> 

How I can do that?

**Tags:** r, differential-expression, deseq2
> **Comments:**
> **username_1**: Just make a heatmap?  
> **username_0**: Then from a data frame with 2632 genes, how I select a list of genes for heatmap? Because a heatmap with 2632 genes is not clear while my main purpose is to shows a list of highly expressed genes across my samples  
> **username_1**: select the N genes with the highest average expression across all samples?  

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## 0 answers

