Question: how to normalise/Scale the FPKM and Ka/Ks value in a matrix?
0
gravatar for Ares Cao
5.6 years ago by
Ares Cao20
Shanghai China
Ares Cao20 wrote:

I've got two columns about RNA-seq FPKM between two species and a ka/ks column of these ortholog,  I want to draw a heatmap to see  if there are some patterns, but the range of FPKM is quite broad (0~10000) and Ka/Ks value is 0~3, Is there some ways to scale the value in these three columns and draw a heatmap to see some pattern?

Great thanks !

kaks rna-seq evolutionary R • 1.7k views
ADD COMMENTlink modified 5.6 years ago by Irsan7.0k • written 5.6 years ago by Ares Cao20
0
gravatar for Irsan
5.6 years ago by
Irsan7.0k
Amsterdam
Irsan7.0k wrote:

At first, use log-transformed FPKM values. Second, see the scale()-function included in the base functionality of R
 

ADD COMMENTlink written 5.6 years ago by Irsan7.0k

Thanks , that could be helpful!

ADD REPLYlink written 5.6 years ago by Ares Cao20
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