This is not a BioC issue in itself, but I thought some people might find it interesting. I was using the 'cor' function to get correlation coefficients for the slides (2-colour cDNA) in some experiments I am analysing, and I found an interesting (to me, at least) difference in the background correlations that seems related to the scanner used. I got the coefficients comparing both foregrounds, both backgrounds, and each foreground to its background. Both foregrounds show a high correlation in all my slides, indicating that most genes do not change, as expected. The foreground/background correlations are low... which is good too, but the actual numbers vary acording to the scanner used. The slides that were scanned with an ArrayWorx scanner give coefficients around 0.10-0.15. Those that were scanned with a Perkin Elmer ScanArray 5000 give me coefficients of around 0.03-0.10. Finally, those scanned with an Axon 4200 give me coefficients of 0.01-0.04. I always thought the background was best on the Axon ones, although the signals seemed "nicer" on the ArrayWorx. Hmmm... That's all. Jose -- Dr. Jose I. de las Heras Email: J.delasHeras at ed.ac.uk The Wellcome Trust Centre for Cell Biology Phone: +44 (0)131 6513374 Institute for Cell & Molecular Biology Fax: +44 (0)131 6507360 Swann Building, Mayfield Road University of Edinburgh Edinburgh EH9 3JR UK