On Tue, Oct 1, 2013 at 10:56 AM, James W. MacDonald <jmacdon at="" uw.edu=""> wrote: > Hi Leif, > > Here is some code I use to do this. Here I assume you have both an > ExpressionSet called 'eset' and a PLMset called 'plm'. I usually use oligo, > so in my case it is an oligoPLM object, but no matter. > > sn <- gsub("\\.CEL", "", sampleNames(eset)) > ## don't re-make existing plots > if(!all(file.exists(paste(sn[length(sn)], "png", sep = ".")))) { > sn <- sn[!file.exists(paste(sn[length(sn)], "png", sep = "."))] > for(i in seq_len(length(sn))){ > png(paste0(sn[i], "png")) > image(plm, type = "residuals", which = i) > dev.off() > } > } FYI, with the 'R.devices' package the above can be done as: library("R.devices") ## don't re-make existing plots options("devEval/args/force"=FALSE) sn <- gsub("\\.CEL", "", sampleNames(eset)) for(i in seq_along(sn)) { toPNG(sn[i], { image(plm, type="residuals", which=i) }) } Adjust aspect ratio by specifying argument 'aspectRatio' for toPNG(). A completely different path is to use aroma.affymetrix, e.g. library("aroma.affymetrix") csR <- AffymetrixCelSet$byName("GSE9890", chipType="HG-U133_Plus_2") res <- doRMA(csR, drop=FALSE, verbose=TRUE) rs <- calculateResidualSet(res$plm, verbose=TRUE) ae <- ArrayExplorer(rs) setColorMaps(ae, c("log2,log2neg,rainbow", "log2,log2pos,rainbow")) process(ae, interleaved="auto", verbose=TRUE) display(ae) That will generate PNGs where each probe on the array occupies exactly one pixel. These PNGs can be navigated via the ArrayExplorer. See the residual ArrayExplorer example on http://aroma-project.org/demos/ for an example. /Henrik > > > Best, > > Jim > > > > On Tuesday, October 01, 2013 1:43:37 PM, Peterson, Leif wrote: >> >> We are interested in saving all the AffyPLM residual plots to disk (in a >> single folder) but cannot find syntax in the user's guide or in forums on >> how to do this. Thx ahead of time, LP >> >> Houston Methodist. Leading Medicine. >> >> Ranked by U.S.News & World Report as one of America's "Best Hospitals" in >> 13 specialties. Named to FORTUNE? Magazine's "100 Best Companies to Work >> For?" list eight years in a row. Designated as a Magnet hospital for >> excellence in nursing. Visit us at houstonmethodist.org. Follow us at >> twitter.com/MethodistHosp and www.facebook.com/HoustonMethodist >> >> ***CONFIDENTIALITY NOTICE*** This e-mail is the property of Houston >> Methodist Hospital and/or its relevant affiliates and may contain restricted >> and privileged material for the sole use of the intended recipient(s). Any >> review, use, distribution or disclosure by others is strictly prohibited. If >> you are not the intended recipient (or authorized to receive for the >> recipient), please contact the sender and delete all copies of the message. >> Thank you. >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor > > > -- > James W. MacDonald, M.S. > Biostatistician > University of Washington > Environmental and Occupational Health Sciences > 4225 Roosevelt Way NE, # 100 > Seattle WA 98105-6099 > > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor