Question: how to normalise/Scale the FPKM and Ka/Ks value in a matrix?
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gravatar for Ares Cao
4.9 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 • 1.6k views
ADD COMMENTlink modified 4.9 years ago by Irsan6.8k • written 4.9 years ago by Ares Cao20
0
gravatar for Irsan
4.9 years ago by
Irsan6.8k
Amsterdam
Irsan6.8k wrote:

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

ADD COMMENTlink written 4.9 years ago by Irsan6.8k

Thanks , that could be helpful!

ADD REPLYlink written 4.8 years ago by Ares Cao20
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