Hi All: I am using Agilent 44k chips to detect Gene expression in different treatment groups to a common reference.

The common reference is dye swapped. I have at least three arrays for each treatment and total 5 treatments.

Treatment groups are specified at the targets file then i use (readtargets to identify groups) when i use the Tquantile to normalize beween arrays data is still not normalized.

Where could the error be?

Thanks 

Why did you decide to use Tquantile normalization and what did you expect it to do?

Are you attempting a separate channel analysis? If not, there is no need for between arrays normalization.

Most likely, the problem is that you have chosen to use Tquantile for a purpose that it was not intended. It is a method that should only be used if you really know what you're doing. Why not use a more standard normalization method, perhaps following one of the examples in the limma User's Guide?