It seems I can't send attachments, I copy the codes here.


test_plotLocation_affy.R

#!/usr/bin/env Rscript
#kristof.jakab@hegelab.org

# 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 744Ă---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.


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