Thanks Everyone for your help, I got many replies. Most had built their own annotation, thinking that BioC packages had only Affymetrix annotation. However thanks a million to James who pointed to the BioC builds of Agilent annotation. There many BioC builds for Agilent chips including the human chips g4100a, g4101a, g4110b, g4111a and g4112a. There is also mouse and other species annotation. For other who like myself had not matched these up, there is a list of the Agilent array names is available at http://www.chem.agilent.com/scripts/generic.asp?lpage=5175&indcol=N&pr od col=Y. I needed the 44K whole genome human Agilent chip (the double density one), this is G4112A. Hence the BioC package is for this is hgug4112a. Hope this is helpful to others like myself who were confused. Aedin