[BioC] MAPlot

[Gordon Smyth]

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 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