I am quite new to limma and need to ask how to export the normalized data. I want to use them in graphical data exploration and presenatation. So, I do something like this (following the Mattick Lab post):
library(limma) targets <- readTargets('targets.txt') x <- read.maimages(targets, path = 'mydirectory', source = 'agilent', green.only =T) y <- backgroundCorrection(x,method = 'normexp') y <- normalizeBetweenArrays(y, method = 'quantile')
So I guess 'y' now contains the log2 expression data.
Question: how can I get them out of R and into a, say, tab-delimited text file?
I would be much obliged.