Question: how to make gene cluster from RNA-Seq counts?
0
gravatar for ahmad.moousavi
9 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 • 238 views
ADD COMMENTlink modified 9 months ago by Michael Love24k • written 9 months ago by ahmad.moousavi0
Answer: how to make gene cluster from RNA-Seq counts?
0
gravatar for Michael Love
9 months ago by
Michael Love24k
United States
Michael Love24k 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 9 months ago by Michael Love24k

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 9 months ago • written 9 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 9 months ago by Michael Love24k

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

Thanks anyway.

 

ADD REPLYlink written 9 months ago by ahmad.moousavi0
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 144 users visited in the last hour