Question: Presenting differential expression data containing infinite log2(Fold Change)s
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gravatar for jammydodger123456
21 months ago by
jammydodger12345620 wrote:

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 • 868 views
ADD COMMENTlink modified 21 months ago by Satyajeet Khare1.3k • written 21 months ago by jammydodger12345620

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.

ADD REPLYlink written 21 months ago by Santosh Anand4.7k
1
gravatar for Satyajeet Khare
21 months ago by
Satyajeet Khare1.3k
Pune, India
Satyajeet Khare1.3k wrote:

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

ADD COMMENTlink written 21 months ago by Satyajeet Khare1.3k
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