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Old 09-05-2012, 01:41 PM   #1
mlkerber
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Default 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.
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Old 09-06-2012, 12:41 AM   #2
Simon Anders
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Usually, log2 fold changes are given, i.e., -2 means a reduction 2^-2, i.e., to a quarter.
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Old 09-06-2012, 05:45 AM   #3
mlkerber
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Thank you! That seems to agree with the documentation that I found for edgeR.
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