Extract log2FC values from volcanoplot() possible?
1
0
Entering edit mode
17 months ago
appropiate ▴ 80

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 • 480 views
ADD COMMENT
3
Entering edit mode
17 months ago
Gordon Smyth ★ 5.4k

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

See help("MArrayLM-class")

ADD COMMENT

Login before adding your answer.

Traffic: 1102 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6