R: Confused about Limma R package output being LogFC or Log2FC
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Keith • 0
@e30d7f37
Last seen 8 days ago
United States

Hello community,

I was running Limma on RNA array expression data and am confused about the output of Limma toptable(). One of the columns is called LogFC, but I want to report Log2FC. After searching some Bioconductor posts and the Limma vignette, I've found conflicting reports on where Limma is reporting a true LogFC or Log2FC. Can someone help clarify?

If Limma output is a true LogFC, using R, how can I convert a LogFC into Log2FC? I am also very new to this type of analysis so any short or deep answers will be greatly appreciated.

limma R ExpressionData • 96 views
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@gordon-smyth
Last seen 4 minutes ago
WEHI, Melbourne, Australia

The output from limma topTable() is log2. If you type help("topTable") then the documentation says:

logFC: estimate of the log2-fold-change corresponding to the effect or contrast

The limma User's Guide says:

A number of summary statistics are presented by topTable() for the top genes and the selected contrast. The logFC column gives the value of the contrast. Usually this represents a log2-fold change between two or more experimental conditions although sometimes it represents a log2-expression level.

The fact that limma gives log2 results is mentioned many times in the documentation. I don't know of any conflicting documentation or reports. If you point out an incorrect statement we'll fix it.

BTW, the abbreviated "logFC" notation isn't intended to imply a particular base and would be correct if the logs were base-2 or base-e or base-10 (https://en.wikipedia.org/wiki/Logarithm). In the limma context, it's always log2 so there's no ambiguity.

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Thank you for clearing that up, especially with the abbreviation