I have two sets of CEL files: one from MOE430A and one from MOE4302. I would like to normalize similar probe sets across the chip types but I am unable to combine Affybatches as they are different sizes. This was touched on previously in this list serve concerning the combination of HGU133A and HGU133 Plus2.0 chips. I could not, however, find an answer to the problem in this thread. I was thinking I could restructure the existing MOE4302 affybatch by subtracting/removing the MOE430B probe set data and then proceed to combining this with the existing MOE430A affybatch. I am able to perform routine R manipulations but the subtracting scheme detailed above is beyond my scope. Scott Ochsner, Ph.D. Huffington Center on Aging, M810 Baylor College of Medicine Houston, TX. 77030 Lab: 713-798-1620 Office: 713-798-1585 [[alternative HTML version deleted]]

Scott Ochsner wrote: > I have two sets of CEL files: one from MOE430A and one from MOE4302. I > would like to normalize similar probe sets across the chip types but I am > unable to combine Affybatches as they are different sizes. This was touched > on previously in this list serve concerning the combination of HGU133A and > HGU133 Plus2.0 chips. I could not, however, find an answer to the problem > in this thread. Can you be more be more specific about "unable to combine Affybatches as they are different sizes"? Did you try the function combineAffyBatcg from package matchprobes? Bw Wolfgang -- ------------------------------------- Wolfgang Huber European Bioinformatics Institute European Molecular Biology Laboratory Cambridge CB10 1SD England Phone: +44 1223 494642 Http: www.dkfz.de/abt0840/whuber