Dear all,

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.

Thank you.

jd

The object you are calling 'y' is an EList, and y$E contains the normalized data. So you could hypothetically use write.table() to output to a file. But I would recommend that you resist this temptation. There are any number of Bioconductor packages (one of which is limma, the package you are currently using) that are useful for exploration and presentation of your data.

In fact I would argue that the easiest and most productive way for you to proceed from here is to keep your data in R and finish the analysis using limma. I can't imagine what you would do with those data that you couldn't do (probably more efficiently) with Bioconductor.

If you say what exactly you are trying to do, I am sure we can come up with some pointers.