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
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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
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