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Presenting differential expression data containing infinite log2(Fold Change)s

I have differential expression data for my genes of interest which I would like to present in heatmaps, graphs etc. The standard value used for this seems to be the log2(FC). However, when the FPKM for genes go from 0 to x and from x to 0, this is problematic. Does anyone know how to present data containing these 'infinite' log2(FC)s? I've seen some mentions of simply adding a very small number and then calculating the log2(FC), but I wasn't sure if that is generally accepted.

rna-seq
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updated by Satyajeet Khare Satyajeet Khare • written by jammydodger123456 • jammydodger123456

Which tool did you use for differential analysis? The chances are very high that the final output is already log2(FC). On the other hand, adding a tiny number to avoid taking log of zero is quite accepted.

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written by Santosh Anand Santosh Anand

1 answer

A pseudocount of 1 can be added to the raw count matrix. FPKMs and TPMs and log changes can be calculated from there on.

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written by Satyajeet Khare Satyajeet Khare

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