Hi! I am going to analyze data from an cDNA microarray experiment conducted to compare "diseased" and "healthy" pigs. The experiment has been conducted as a "classical common reference" experiment with the reference labeled with the same dye on all slides. A total of 24 animals are included in the experiment (12 "diseased" and 12 "healthy"). Question: one of the "diseased" and one of the "healthy" animals have been replicated three times resulting in a total of 28 slides. How should this replication be handled in the analysis using LIMMA? Looking forward hearing from you! Jakob ------------------------------------------------------------------- Jakob Hedegaard Danish Institute of Agricultural Sciences Department of Genetics and Biotechnology Molecular Genetics and System Biology Building K25 Research Centre Foulum P.O. box 50 DK-8830 Tjele Denmark Tel: (+45)89991363 Fax: (+45)89991300 [[alternative HTML version deleted]]

> Date: Fri, 4 Mar 2005 08:58:01 +0100 > From: "Jakob Hedegaard" <jakob.hedegaard@agrsci.dk> > Subject: [BioC] LIMMA: uneven replication of samples > To: <bioconductor@stat.math.ethz.ch> > > Hi! > > I am going to analyze data from an cDNA microarray experiment conducted > to compare "diseased" and "healthy" pigs. > > The experiment has been conducted as a "classical common reference" > experiment with the reference labeled with the same dye on all slides. A > total of 24 animals are included in the experiment (12 "diseased" and 12 > "healthy"). > > Question: one of the "diseased" and one of the "healthy" animals have > been replicated three times resulting in a total of 28 slides. > > How should this replication be handled in the analysis using LIMMA? How far have you got with reading the documentation? This is called "technical replication" and there's a section on it in the Limma User's Guide. But, really, with only two of the animals replicated, if your purpose is to find differentially expressed genes, it would be simpler and probably equally good to just choose the best quality slide for those each of those two animals and discard the other two. Gordon > Looking forward hearing from you! > Jakob > > ------------------------------------------------------------------- > Jakob Hedegaard > Danish Institute of Agricultural Sciences > Department of Genetics and Biotechnology > Molecular Genetics and System Biology > Building K25 > Research Centre Foulum > P.O. box 50 > DK-8830 Tjele > Denmark > Tel: (+45)89991363 > Fax: (+45)89991300