[Bioc-devel] question about affy::plotLocation
kristof.jakab at hegelab.org
Mon Jun 16 10:59:35 CEST 2014
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.)
I've linked 2 files to this email:
Mozilla Thunderbird <http://www.getthunderbird.com> makes it easy to
share large files over email.
More information about the Bioc-devel