It seems I can't send attachments, I copy the codes here.
test_plotLocation_affy.R #!/usr/bin/env Rscript #[email protected] # MAKE AFFYBATCH #---------------------------------------------------------- # download CEL file library(GEOquery) getGEOSuppFiles("GSM229005") #---------------------------------------------------------- # read CEL file library(affy) geoS <- ReadAffy(filenames=paste("GSM229005","GSM229005.CEL.gz", sep="/")) # PLOTTING TO PNG #---------------------------------------------------------- # raw png(filename="geo_testing_spot_locations_raw.png",height=744*10,width=744*10,res=1200) ## image (log scale intensities) image(geoS,transfo=log) ## perfectmatches l <- indexProbes(geoS, which="pm", geneNames(geoS)) lapply(l,function(li){ xy <- indices2xy(li, abatch=geoS) plotLocation(xy,col="tomato",pch=18,cex=0.075) }) ## missmatches l <- indexProbes(geoS, which="mm", geneNames(geoS)) lapply(l,function(li){ xy <- indices2xy(li, abatch=geoS) plotLocation(xy,col="aquamarine",pch=18,cex=0.075) }) dev.off() #---------------------------------------------------------- # mirrored png(filename="geo_testing_spot_locations_mirrored.png",height=744*10,width=744*10,res=1200) ## image (log scale intensities) image(geoS,transfo=log) ## perfectmatches l <- indexProbes(geoS, which="pm", geneNames(geoS)) lapply(l,function(li){ xy <- indices2xy(li, abatch=geoS) xy <- cbind(x=xy[,1],y=(743-xy[,2])) # mirroring plotLocation(xy,col="tomato",pch=18,cex=0.075) }) ## missmatches l <- indexProbes(geoS, which="mm", geneNames(geoS)) lapply(l,function(li){ xy <- indices2xy(li, abatch=geoS) xy <- cbind(x=xy[,1],y=(743-xy[,2])) # mirroring plotLocation(xy,col="aquamarine",pch=18,cex=0.075) }) dev.off() correction_for_plotLocation.R plotLocation <- function(x, col="green", pch=22, ...) { if (is.list(x)) { x <- cbind(unlist(lapply(x, function(x) x[,1])), unlist(lapply(x, function(x) x[,2]))) } points(x[,1], 743-x[,2] # mirroring 744Ã---744 matrix, numbered from 0 to 743 , pch=pch, col=col, ...) } On 06/16/2014 10:59 AM, Kristóf Jakab wrote: > Dear BiocDevelR! > > I'm working lot with the excelent *affy package* of Rafael A. > Irizarry, I find it very useful. > > I have a bit strange experience with it's *plotLocation function*. > It seems, *I have to mirror Y coordinates* to plot properly. > Perhaps it's because the CEL file reading starts from the top, and > plotting starts from the bottom. > > I'm not sure if I'm rigtht, can you check, that I haven't made mistake? > If yes, I suggest a (simple) solution for this. > > I attach two plot made from a GEO GSM CEL file (see script). > First I've plotted all gene name (ProbeSet) on the CEL file images, > second I've plotted after mirroring the Y coordinates. > As you can see on the raw plotting there are points on chip name > (printed by BioB spots). > > I attach my plotting script too, and a potential correction for the > affy::plotLocation. (I've tried it, it seems good.) > > Yours sincerly: > Kristóf Jakab > > I've linked 2 files to this email: > geo_testing_spot_locations_mirrored.png > <https://www.box.com/shared/ow3q5sn3fpmyz3u8w533>(6.0 MB)Box > <https://www.box.com/thunderbird>https://www.box.com/shared/ow3q5sn3fpmyz3u8w533 > > > geo_testing_spot_locations_raw.png > <https://www.box.com/shared/3sj9i3lpkixkq85qar0r>(6.1 MB)Box > <https://www.box.com/thunderbird>https://www.box.com/shared/3sj9i3lpkixkq85qar0r > > > Mozilla Thunderbird <http://www.getthunderbird.com> makes it easy to > share large files over email. [[alternative HTML version deleted]]
_______________________________________________ [email protected] mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
