How to analyze aCGH data in R?

Question

[Lila M]

Dear all, I've tried to analyze this data that is a aCGH data in R. But I couldn't find any tutorial that can help me to import data and everything. Any idea? Thank you

[Kevin Blighe]

Hey Lila. limma should be able to do it. Have you checked that out?

[Lila M]

Hi Kevin, and thank you for your feed back. Yes I've checked it and found something related with Agilent4x44K Arrays however, this experiment is CGH array (4X180K) so I could not find something related with CGH arrays, any clue about how to start with it? Thanks!

[Kevin Blighe]

I'm not sure - I thought that limma had general functionality for Agilent arrays, though (both single and two-colour arrays). I wish that I had more time to check myself; otherwise, you can obtain the normalised data with the following code:

library(Biobase)
library(GEOquery)

# load series and platform data from GEO
gset <- getGEO("GSE36864", GSEMatrix =TRUE, getGPL=FALSE)
if (length(gset) > 1) idx <- grep("GPL8687", attr(gset, "names")) else idx <- 1
gset <- gset[[idx]]

With that, you can do DEA and any other downstream stuff.