Clarification of edgeR logFC

mlkerber · 09-05-2012, 02:41 PM

Hi everyone,
I'm completely new to RNAseq and was hoping someone could help me understand the data output by edgeR. Specifically, could someone explain what the logFC number actually means? I understand that a bigger number means a larger difference in the expression of a gene, but is it literally the log of the fold change?

For example, does a logFC of 2 actually mean a fold change of 10^2? In that case, does a logFC of -2 mean a fold change of 10^-2 or -10^2?

I've been assuming that large, negative logFC numbers meant a large downregulation of that gene in our test sample vs control, but when this interpretation of logFC occurred to me, I became very worried that the expression of these genes was only very slightly different!

Any help would be appreciated.

Simon Anders · 09-06-2012, 01:41 AM

Usually, log2 fold changes are given, i.e., -2 means a reduction 2^-2, i.e., to a quarter.

mlkerber · 09-06-2012, 06:45 AM

Thank you! That seems to agree with the documentation that I found for edgeR.

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09-05-2012, 02:41 PM	#1
mlkerber Junior Member Location: North Carolina Join Date: Sep 2012 Posts: 3	Clarification of edgeR logFC Hi everyone, I'm completely new to RNAseq and was hoping someone could help me understand the data output by edgeR. Specifically, could someone explain what the logFC number actually means? I understand that a bigger number means a larger difference in the expression of a gene, but is it literally the log of the fold change? For example, does a logFC of 2 actually mean a fold change of 10^2? In that case, does a logFC of -2 mean a fold change of 10^-2 or -10^2? I've been assuming that large, negative logFC numbers meant a large downregulation of that gene in our test sample vs control, but when this interpretation of logFC occurred to me, I became very worried that the expression of these genes was only very slightly different! Any help would be appreciated.

09-06-2012, 01:41 AM	#2
Simon Anders Senior Member Location: Heidelberg, Germany Join Date: Feb 2010 Posts: 994	Usually, log2 fold changes are given, i.e., -2 means a reduction 2^-2, i.e., to a quarter.

09-06-2012, 06:45 AM	#3
mlkerber Junior Member Location: North Carolina Join Date: Sep 2012 Posts: 3	Thank you! That seems to agree with the documentation that I found for edgeR.