Question: Presenting differential expression data containing infinite log2(Fold Change)s
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gravatar for jammydodger123456
2.8 years ago by
jammydodger12345630 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 • 1.2k views
ADD COMMENTlink modified 2.8 years ago by Satyajeet Khare1.5k • written 2.8 years ago by jammydodger12345630

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 2.8 years ago by Santosh Anand5.1k
1
gravatar for Satyajeet Khare
2.8 years ago by
Satyajeet Khare1.5k
Pune, India
Satyajeet Khare1.5k 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 2.8 years ago by Satyajeet Khare1.5k
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