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Question: how to make gene cluster from RNA-Seq counts?
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gravatar for ahmad.moousavi
8 weeks ago by
ahmad.moousavi0 wrote:

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.

 

ADD COMMENTlink modified 8 weeks ago by Michael Love20k • written 8 weeks ago by ahmad.moousavi0
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gravatar for Michael Love
8 weeks ago by
Michael Love20k
United States
Michael Love20k wrote:

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().

ADD COMMENTlink written 8 weeks ago by Michael Love20k

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?

ADD REPLYlink modified 8 weeks ago • written 8 weeks ago by ahmad.moousavi0

I have no code for this.

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

ADD REPLYlink written 8 weeks ago by Michael Love20k

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

Thanks anyway.

 

ADD REPLYlink written 8 weeks ago by ahmad.moousavi0
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