[BioC] MAPlot

[Mohammad Esad-Djou]

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?

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 at 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 at web.de>
> > Subject: Re: [BioC] MAPlot
> > To: bioconductor at stat.math.ethz.ch, ramasamy at 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
> 
>