Question: Report and compare log2FC vs FC
0
gravatar for Catalina Aguilar Hurtado
4.2 years ago by
United States

Hi Michael,

I will like your opinion on reporting FC or log2FC. I use Deseq2 but other people I work with use other programs and report their data in FC so I usually convert my data to FC.

res$FC <- logratio2foldchange(res$log2FoldChange, base=2) 

Is there any reason why we should use one or the other? or is just a matter of personal likes?

Thanks

Catalina

 

deseq2 logfc • 11k views
ADD COMMENTlink modified 4.2 years ago by smoorthie10 • written 4.2 years ago by Catalina Aguilar Hurtado50
Answer: Report and compare log2FC vs FC
2
gravatar for Ryan C. Thompson
4.2 years ago by
The Scripps Research Institute, La Jolla, CA
Ryan C. Thompson7.3k wrote:

I personally prefer log2 fold change, because of the symmetry: +1 is twofold up, and -1 is twofold down, etc. But many biologists are not comfortable thinking in log space and prefer just fold changes. Either way, it's the same information.

If you want to report non-log fold changes but still preserve the symmetry, you can convert "2" to "2-fold up" and "0.5" to "2-fold down".

ADD COMMENTlink written 4.2 years ago by Ryan C. Thompson7.3k

Hi Ryan thanks for your reply. Don't really understand how to preserve the symmetry, what do you mean by 2-fold up or down?

ADD REPLYlink written 4.2 years ago by Catalina Aguilar Hurtado50
1

I mean that "2-fold up" and "2-fold down" are conceptually of equal magnitude (i.e. symmetric), But their corresponding fold changes, 2 and 0.5, are not, while their corresponding log2 fold changes, +1 and -1, are.

ADD REPLYlink written 4.2 years ago by Ryan C. Thompson7.3k
Answer: Report and compare log2FC vs FC
1
gravatar for smoorthie
4.2 years ago by
smoorthie10
smoorthie10 wrote:

If you are going to plot the data (as opposed to just quoting values) then I think Ryan's argument about symmetry is even stronger. Plotted naively a 100-fold up-regulated gene looks like a much bigger effect than a 0.01-fold down-regulated gene. Of course then the answer (if you have to quote fold changes rather than log2 fc) is simply to plot with a log-scale.

ADD COMMENTlink written 4.2 years ago by smoorthie10
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