Question

how to make gene cluster from RNA-Seq counts?

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ahmad.moousavi • 0

@ahmadmoousavi-14701

Last seen 6.1 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 • 1.0k views

ADD COMMENT • link updated 6.1 years ago by Michael Love 43k • written 6.1 years ago by ahmad.moousavi • 0

score 0 · Answer 1 · 2018-10-12

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Michael Love 43k

@mikelove

Last seen 3 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().

ADD COMMENT • link 6.1 years ago Michael Love 43k

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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?

ADD REPLY • link 6.1 years ago ahmad.moousavi • 0

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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.

ADD REPLY • link 6.1 years ago Michael Love 43k

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

Thanks anyway.

ADD REPLY • link 6.1 years ago ahmad.moousavi • 0