Hi Kristóf,
On 6/16/2014 10:20 AM, Kristóf Jakab wrote:
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, ...)
}
Thanks for pointing this out. It's apparent almost nobody ever uses this
code, as it has been in the affy package since pretty much the beginning
(2002), and you are the first to notice this.
Unfortunately, hard-coding the number of rows isn't the answer, since
Affy arrays have different dimensions. Probably the best fix is to add
an additional required argument 'affybatch' that we can use to extract
the chip dimensions from.
Best,
Jim
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]]
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James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
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