Hi, I have been using rma on Affy chips and have faced a problem that some of the experiments are done on MgU74A chips (which have some genes masked) and some on MgU74A V2 chips. I would really appreciate any suggestions on how I could normalise two types of chips together. Regards Marg

Hi Marg, have a look at the function 'combine' in the package 'matchprobes'. Try ? combine openVignette("matchprobes") The documentation is somewhat sketchy, and it probably requires some understanding of the inner workings of the affy package to run it. Let me know if you have questions Best wishes Wolfgang ------------------------------------- Wolfgang Huber Division of Molecular Genome Analysis German Cancer Research Center Heidelberg, Germany Phone: +49 6221 424709 Fax: +49 6221 42524709 Http: www.dkfz.de/mga/whuber ------------------------------------- On Wed, 3 Sep 2003, Margaret Gardiner-Garden wrote: > Hi, > > I have been using rma on Affy chips and have faced a problem that some of > the experiments are done on MgU74A chips (which have some genes masked) and > some on MgU74A V2 chips. I would really appreciate any suggestions on how I > could normalise two types of chips together. > > Regards > Marg >