how to normalise/Scale the FPKM and Ka/Ks value in a matrix?

Question

[Ares Cao]

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 !

Answer 1

[Irsan]

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

[Ares Cao]

Thanks , that could be helpful!