Hello everyone,

It is my first post here. Today I've been asked to perform a Differential gene epression analysis between two groups of normal vs treatment. The analysis was performed with an Illumina MicroArray.

Till now I've performed limma analysis using GES GEO files in quite a simple way, but today I've been ask to work on a file like this:

data.txt

ID_REF  Sample-A1   Sample-A2   Sample-A3   Sample-A4
ILMN_1343291    120.5   122.7   118.9   135.6
ILMN_1343295    257.6   205.6   738.8   433.7
ILMN_1651199    2333    2059.6  1484.3  3195.2
etc...

I'm searching in the Limma manual but I couldn't find how to load this file to perform my analysis. I think this is a expression matrix extracted from a GES file...but I'm not sure.

Do you have any tips for me ? Thanks

The limma package is quite happy to analyze a matrix of expression values. See ?lmFit. You would of course want to convert that data.frame to a matrix, probably with the first column used as the rownames of the matrix.

It is unfortunate that your collaborators have discarded the control probe information provided by the Illumina arrays. Nevertheless you can still do a pretty good job. Just treat the data as generic microarray intensities. You can read and normalize the data by

library(limma)
yraw <- read.delim("data.txt", row.names=1)
y <- backgroundCorrect(yraw, method="normexp")
y <- normalizeBetweenArrays(y, method="quantile")

and you're ready to go.