Hello, I'm working with Arraystar lncRNA microarray for the first time. I tried to normalize the raw files (.txt) using the following script, which I used to normalize different other Agilent chip versions previously. Can anyone please tell me is this ok for Arraystar chip also? Unfortunately, I'm not being able to get the normalized values similar to that provided by the company. The company performed quantile normalization of the raw data using GeneSpring GX.

Here is my script for quantile normalizaiton:

library(limma)

library(limmaGUI)

targets