how to make gene cluster from RNA-Seq counts?
1
0
Entering edit mode
@ahmadmoousavi-14701
Last seen 5.5 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 • 844 views
ADD COMMENT
0
Entering edit mode
@mikelove
Last seen 12 hours 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().

ADD COMMENT
0
Entering edit mode

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 REPLY
0
Entering edit mode

I have no code for this.

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

ADD REPLY
0
Entering edit mode

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

Thanks anyway.

 

ADD REPLY

Login before adding your answer.

Traffic: 866 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6