Question: how to make gene cluster from RNA-Seq counts?
0
gravatar for ahmad.moousavi
12 months 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.

 

rnaseq deseq2 R • 284 views
ADD COMMENTlink modified 12 months ago by Michael Love25k • written 12 months ago by ahmad.moousavi0
Answer: how to make gene cluster from RNA-Seq counts?
0
gravatar for Michael Love
12 months ago by
Michael Love25k
United States
Michael Love25k 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 12 months ago by Michael Love25k

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 12 months ago • written 12 months 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 12 months ago by Michael Love25k

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

Thanks anyway.

 

ADD REPLYlink written 12 months ago by ahmad.moousavi0
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