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

[Giulio Di Giovanni]

Thanks a lot,

I've read the help files and the R and BioC manuals too (and googled too), 
apparently I didn't understand the  suggestions...sorry...I don't' know what 
to say...

Now everything is ok. Well, I discovered that characters following "%" in 
file name have special meanings...(adding spaces etc etc)
There's somewhere a list of these characters and their meanings, others that 
"%3d" ?
Sorry again if I'm bothering you all, that's just that I always like to 
fully know what I'm doing...

thX again


Giulio






>From: "James W. MacDonald" <jmacdon at med.umich.edu>
>To: bioconductor at stat.math.ethz.ch
>Subject: Re: [BioC] How to save jpegs of all MAplots of an affybatch
>Date: Wed, 23 Nov 2005 11:56:54 -0500
>
>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.
>
>Not a stupid question per se, but one that you *might* have been able to
>answer by a close reading of the relevant help files, or alternatively
>by RSiteSearch("jpeg multiple files")
>
>  From ?jpeg:
>
>filename: the name of the output file, up to 511 characters.  The page
>            number is substituted if a C integer format is included in
>            the character string, as in the default.  (The result must be
>            less than 600 characters long.  See 'postscript' for further
>            details.)
>
>  From ?postscript:
>
>   file: a character string giving the name of the file.  If it is
>            '""', the output is piped to the command given by the
>            argument 'command'.
>
>            For use with 'onefile=FALSE' give a 'printf' format such as
>            '"Rplot%03d.ps"' (the default in that case).
>
>So if you simply did
>
>jpeg()
>MAplot(mysamples)
>dev.off()
>
>you would end up with n jpeg files in your working directory named
>Rplot001.jpg
>Rplot002.jpg
>...
>Rplot00n.jpg
>
>If you really don't want these names, you could try your second attempt,
>but add these two lines after the call to jpeg()
>
>medchip <- rowMedians(log2(intensity(mysamples)[pms,]))
>MAplot(mysamples[,i], ref=medchip)
>
>Best,
>
>Jim
>
>
>
>
> >
> > 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
> >
> > _______________________________________________
> > Bioconductor mailing list
> > Bioconductor at stat.math.ethz.ch
> > https://stat.ethz.ch/mailman/listinfo/bioconductor
>
>
>--
>James W. MacDonald
>Affymetrix and cDNA Microarray Core
>University of Michigan Cancer Center
>1500 E. Medical Center Drive
>7410 CCGC
>Ann Arbor MI 48109
>734-647-5623
>
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