how to decide which values to use in heatmap2 for plotting FPKM values from RNASeq?

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7.3 years ago

JP • 0

Hi all,

Can anyone please explain me why is FPKM value is converted to log10 (FPKM)+1 or log2 (FPKM) when creating a heatmaps? Is it just for scaling purpose? Why is +1 added in {log10 (FPKM)+1} Some heatmaps use log10 (FPKM)+1 and some use log2 (FPKM), how does one decide which one to use?

Thanks a lot.

heatmap RNA-Seq • 3.9k views

ADD COMMENT • link 7.3 years ago by JP • 0

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log10(FPKM +1) is used to avoid taking log(0) which doesn't work.

ADD REPLY • link 7.3 years ago by WouterDeCoster 47k

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Thank you. But why +1, is it for scaling purpose? And when to use log2FPKM and when to use log10(FPKM +1) ?

ADD REPLY • link 7.3 years ago by JP • 0

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FPKM+1 because you'll take the log of this value and if there are 0 counts for that gene, log(0) is undefined. Therefore you add a small value.

ADD REPLY • link 7.3 years ago by WouterDeCoster 47k

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Sorry for the late reply. Thank you very much

ADD REPLY • link 7.3 years ago by JP • 0

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