At 12:29 AM 1/04/2005, Mohammad Esad-Djou wrote: >Hello, > >I would like Compare 1. experiment with set of experiments 2 to 7 and wrote: > >library(limma) >plotMA(data.exprs, array=1, xlab = "A", ylab="M", main="Gene Signal M/A Plot") > >is Ok? Yes. It actually compares 1 with the median of all. Gordon >Thanks, >Mohammad Esad-Djou > > > > > > library(limma) > > plotMA(data.exprs, array=3) > > > > if you want to compare the 3rd experiment, say, with the others? > > > > Gordon > > > >smyth@wehi.EDU.AU schrieb am 30.03.05 14:05:26: > > > > > Date: Tue, 29 Mar 2005 19:33:54 +0100 > > > From: "Mohammad Esad-Djou" <shahrgol@web.de> > > > Subject: Re: [BioC] MAPlot > > > To: bioconductor@stat.math.ethz.ch, ramasamy@cancer.org.uk > > > > > > Thanks for your help. > > > > > > > > > I have two other questions. > > > > > > 1. How can I compare an experiment correctly with a set of > experiments in ma.plot? > > > > > > is this Ok? (for 7 Expriments) > > > > No it isn't. > > > > > mat <- exprs( data.exprs ) > > > > > > ma.plot( mat[ , 1] + (mat[ , 2] + mat[ ,3] + mat[ ,4]+ mat[ ,5]+ mat[ > ,6]+ mat[ ,7]), mat[ , 1] - > > > (mat[ ,2] - mat[ ,3] - mat[ ,4] - mat[ ,5] - mat[ ,6] - mat[ ,7]) ) > > > > Why not > > > > library(limma) > > plotMA(data.exprs, array=3) > > > > if you want to compare the 3rd experiment, say, with the others? > > > > Gordon > > > > > 2. How can I save the result of ma.plot directly into a file (e.g. > png or JPG...)? > > > > > > > > > Thanks, > > > Mohammad Esad-Djou