how to normalise/Scale the FPKM and Ka/Ks value in a matrix?
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7.7 years ago
Ares Cao ▴ 20

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 !

RNA-Seq evolutionary kaks R • 2.1k views
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7.7 years ago
Irsan ★ 7.4k

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

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Thanks , that could be helpful!

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