[Bioc-devel] question about affy::plotLocation

Kristóf Jakab kristof.jakab at hegelab.org
Mon Jun 16 10:59:35 CEST 2014

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

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