Dear Torsten, There is no need to fool the software as to the real nature of your data. Please do not do this. Simply use modelMatrix(targets, ref="Ref") where "Ref" is the name of your reference sample. Then limma will compute all quantities correctly relative to the reference regardless of what dye was used. Best wishes Gordon > Date: Wed, 10 Jun 2009 11:07:23 +0100 > From: "michael watson \(IAH-C\)" <michael.watson at="" bbsrc.ac.uk=""> > Subject: Re: [BioC] Change M-value calculation from red/green to > green/red > To: "Torsten Waldminghaus" <torsten.waldminghaus at="" rr-research.no="">, > <bioconductor at="" stat.math.ethz.ch=""> > > Multiply by -1 > > -----Original Message----- > From: bioconductor-bounces at stat.math.ethz.ch > [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Torsten > Waldminghaus > Sent: 10 June 2009 10:59 > To: bioconductor at stat.math.ethz.ch > Subject: [BioC] Change M-value calculation from red/green to green/red > > Dear all, > > I started using the limma library to deal with microarray data. The > available functions are really helpful to do normalization like this: > > RG <- read.maimages(files,"agilent") > RG.b <- backgroundCorrect(RG,method="minimum") > MA.p <-normalizeWithinArrays(RG.b,method="loess") > MA.pAq <- normalizeBetweenArrays(MA.p, method="Aquantile") > > However, in my experiments I had the reference sample labeled in green > so I would like to have M-values calculated as M=log2G-log2R instead of > M=log2R-log2G. Is there any simple way to do this? > > Thanks for any help, > Torsten > > Torsten Waldminghaus > Department of Cell Biology > Institute for Cancer Research > Rikshospitalet-Radiumhospitalet-HF > Ullernchaussen 70 > 0310 Oslo > tel: 47-22935973 > fax: 47-22934580 > e-mail: Torsten.Waldminghaus at rr-research.no > http://openwetware.org/wiki/User:Torsten_Waldminghaus