> Date: Thu, 1 Jun 2006 11:38:02 +0100 > From: "michael watson \(IAH-C\)" <michael.watson at="" bbsrc.ac.uk=""> > Subject: [BioC] Limma, dye-swaps and uneven numbers of replicate > arrays > To: <bioconductor at="" stat.math.ethz.ch=""> > > Hi > > A simple question really - I have five biological replicate RNA samples. > Each will have cells untreated vs treated, so that's five arrays. I > want to do dye-swaps, but that means I can have 2* Cy5/Cy3, and 3* > Cy3/Cy5. Do I need to compensate for this "imbalance"? How do I do it > in limma? > > Thanks > Mick Such imbalance is accomodated automatically, just as is any imbalance in any linear model you might fit. It requires no special action from you. Best wishes Gordon