[BioC] How to handle 2-channel array that is duplicated on a slide

[Noah Cohen]

Hi - I am a Biioconductor neophyte trying to look at data from a
2-channel cDNA microarray that has about 3,000 genes (primarily equine)
related to inflammatory and immune response that have been read using
ImaGene software.  The slides are arranged such that the array is
duplicated on the top and bottom half of the slide (ie, the array of
genes is printed twice on each slide).  

Is there somewhere I can read about how to handle such a slide format,
beginning with exploratory data analysis (such as basic plots) and
normalization?

Thank you - Noah Cohen


Noah D. Cohen, VMD, MPH, PhD, DACVIM
Professor
Department of Large Animal Clinical Sciences
College of Veterinary Medicine and Biomedical Sciences
Texas A&M University
College Station, Texas 77843-4475
Telephone: 979-845-3541
Fax: 979-847-8863
e-mail: ncohen at cvm.tamu.edu