Hi everyone, I have a question concerning spotted array analysis and limma. The analysis is working fine except I'm not sure what the out put means. I have sample A and samlpe B on an array (3 replicate slides) and in limma analysis I put sample A as the reference. Therefore the results I get, are they the genes up/down regulated due to sample A or sample B? Josephine Brennan [[alternative HTML version deleted]]

> Date: Mon, 24 Jan 2005 15:39:57 +0000 > From: Josephine <josephine.brennan@ucd.ie> > Subject: [BioC] limma > To: bioconductor@stat.math.ethz.ch > > Hi everyone, > I have a question concerning spotted array analysis and limma. > The analysis is working fine except I'm not sure what the out put means. > I have sample A and samlpe B on an array (3 replicate slides) and in limma analysis I put sample A > as the reference. > Therefore the results I get, are they the genes up/down regulated due to sample A or sample B? > Josephine Brennan Positive M-value in toptable means up in sample B, negative means down in sample B. That makes sense since you have specified sample A to your reference and hence sample B to be the test sample -- positive means up relative to the reference, negative means down relative to the reference. Gordon

Hi Josephine, Since you already have an answer I was wondering if you could tell me what you mean with having sample A as a reference? Did you define it as the Cy3 labelled sample in the targets file (and if you had a dye- swap what would that mean then?)? Since I was wondering about the meaning of the M-values just like you I am now somewhat confused not knowing exactly what my reference is if I have a dye-swap experiment (pretty much the same as the Bob-example!) Anja [[alternative HTML version deleted]]