how to decide which values to use in heatmap2 for plotting FPKM values from RNASeq?
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.
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log10(FPKM +1) is used to avoid taking log(0) which doesn't work.
Thank you. But why +1, is it for scaling purpose? And when to use log2FPKM and when to use log10(FPKM +1) ?
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.
Sorry for the late reply. Thank you very much