Extract log2FC values from volcanoplot() possible?
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Entering edit mode
13 months ago
appropiate ▴ 60

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!

volcanoplot R limma • 406 views
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Entering edit mode
13 months ago
Gordon Smyth ★ 4.9k

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

See help("MArrayLM-class")

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