James W. MacDonald wrote: > 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) > Correction - this won't work - a closer reading of the code (or Ben's email) would have alerted me to the fact that the ref argument applies to the index of a reference chip rather than a set of reference data. Best, Jim -- 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

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 > >_______________________________________________ >Bioconductor mailing list >Bioconductor at stat.math.ethz.ch >https://stat.ethz.ch/mailman/listinfo/bioconductor