how to make gene cluster from RNA-Seq counts?
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@ahmadmoousavi-14701
Last seen 6.2 years ago

Hi

I have several questions and I appreciate for answer :

1- I wanted to know how can I add cluster analysis like below image based on read count.

 

2- Should I run the code only for the genes with minimum number of reads (e.g rowSum(gene) > 10) or I should run it only for DEGs ?

Tnx.

 

deseq2 rnaseq R • 1.1k views
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@mikelove
Last seen 2 days ago
United States

You can make such clusters from variance stabilized data using vst(). I would remove low count genes. You can remove the mean expression by subtracting out rowMeans() after the vst().

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Thanks Michael, at last one answered.

Would you please share your R code with me?

I used to remove low counts by rowSum > 10 is it working too?

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I have no code for this.

It’s not built in to DESeq2 but you can use hclust and other base R functions.

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thanks, but I need the code !!, I will found the way.

Thanks anyway.

 

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