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.

Thank you for your assistance.

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.