Thanks, I did not notice that difference, but how was bioconductor bgcorrect=MAS method implemented, 10 by 10 or 4 by 4? I did both MAS with Affy software and MAS in bioconductor on the same data set and got quite different results. I wonder if the difference comes from the background correction. L Date: Wed, 29 Sep 2004 08:54:03 -0700 From: Ben Bolstad <> Subject: Re: [BioC] dChip To: Lizhe Xu <lxu@chnola-research.org> Cc: hess@stat.colostate.edu, lgautier@altern.org, bioconductor@stat.math.ethz.ch Message-ID: <1096473243.3004.3.camel@bmbbox.dyndns.org> Content-Type: text/plain Actually I believe that it is a slightly modified version of the MAS background that is used in dChip. They use a 10 by 10 grid rather than 4 by 4. Ben