[BioC] MAPlot

[Gordon K Smyth]

> 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