[BioC] How to save jpegs of all MAplots of an affybatch

[Ben Bolstad]

The easiest way is something like

jpeg("MAplot%03d.jpeg")
MAplot(mysamples)
dev.off()

which would write files MAplot001.jpeg, MAplot002.jpeg, ......



Alternatively, you could use the ref argument to MAplot (to make one of
the arrays the reference) and generate n-1 MAplots using your loop
structure. eg

for(i in 2:n){
jpeg(file=paste(sampleNames(mysamples[,i]),"MAplot.jpeg", sep=""))
MAplot(mysamples[,i],ref=1)
dev.off()



On Wed, 2005-11-23 at 16:09 +0000, Giulio Di Giovanni wrote:
> Hi,
> 
> hoping is not a stupid question,
> I would like to have a jpeg copy of all MAplots I created for my affybatch 
> object.
> 
> jpeg(file=paste(sampleNames(mysamples), anname,".jpeg", sep=""))
> MAplot(mysamples)
> dev.off()
> 
> doesn't work, it writes on the same file all the plots
> 
> and (ovbiously)
> 
> for(i in 1:n){
> jpeg(file=paste(sampleNames(mysamples[,i]),"MAplot.jpeg", sep=""))
> MAplot(mysamples[,i])
> dev.off()
> }
> 
> because to produce a MAplot on an affy chip, you need a median pseudo-chip 
> (i.e. at least two chips)
> 
> Does anyone have an idea/suggestion ?
> 
> Thanks a lot in advance
> 
> Giulio
> 
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-- 
Ben Bolstad <bmb at bmbolstad.com>
http://bmbolstad.com