I am just starting to do microarray analysis. I have been trying to normalize 4 chips (two dye-swap experiments done in biological replicates) After doing backgroundCorrect(method="normexp") , one of the arrays has all of its $G values at NaN. This does not happen when any other method is used. Can someone tell me why this is, and if this can be fixed? Thanks Lance Palmer

You'll see this question asked a few times in the mailing list archives. Try upgrading your version of the limma package. Gordon >Date: Thu, 28 Apr 2005 16:44:41 -0400 >From: "Palmer, Lance" <palmer@cshl.edu> >Subject: [BioC] backgroundCorrect(method="normexp") problems >To: <bioconductor@stat.math.ethz.ch> > >I am just starting to do microarray analysis. I have been trying to >normalize 4 chips (two dye-swap experiments done in biological replicates) > >After doing backgroundCorrect(method="normexp") , one of the arrays has >all of its $G values at NaN. > >This does not happen when any other method is used. > >Can someone tell me why this is, and if this can be fixed? > >Thanks >Lance Palmer