Extract log2FC values from volcanoplot() possible?

Question

[appropiate]

Hello,

An MArrayLM object created with eBayes() from the limma package contains the slot $p.values, which I suppose is used by volcanoplot() to make the volcano plot. Since the volcano plot has log2FC in the x-axis, I suppose volcanoplot() also gets the log2FC values from the MArrayLM object, but how to extract the log2FC values from the MArrayLM object myself?

Thanks!

Answer 1

[Gordon Smyth]

If fit is the MArrayLM object, then the log2-fold-changes are fit$coefficients[, coef].

See help("MArrayLM-class")