> Date: Tue, 28 Feb 2006 15:02:32 +0200 > From: "Ron Ophir" <ron.ophir at="" weizmann.ac.il=""> > Subject: [BioC] Another question about dye swap > To: <bioconductor at="" stat.math.ethz.ch=""> > Message-ID: <s404661c.050 at="" wisemail.weizmann.ac.il=""> > Content-Type: text/plain; charset=US-ASCII > > Hi, >>From limma user guide section 8.1.2 Simple comparisons -> Dye swaps it > is clear that for the following experimental design: > FileName Cy3 Cy5 > File1 wt mu > File2 mu wt > File3 wt mu > File4 mu wt > *(four replicates of two groups (wt , mu) of which two replicates in > each group is labeled by one color(red) the other two is labeled by > another color (green)) > one can estimate the Dye effect by defining that effect as the > intercept : > design <- cbind(DyeEffect=1,MUvsWT=c(1,-1,1,-1)) > fit <- lmFit(MA, design) > fit <- eBayes(fit) > > Let's say that one finds that the Dye effect (for all genes) is > statisticaly insignificant. Would it be correct than to force the model > to go through the intercept by > > design <- cbind(DyeEffect=-1,MUvsWT=c(1,-1,1,-1)) > > Will I get a better estimation of the Mu to wt ratio? > > Thanks, > Ron No. The code you give does not force the model through the intercept and would give erroneous estimates. Simply omitting the DyeEffect column does what you want. Gordon