[BioC] need output to contain probe x, y coordinates on array - AffyTiling

[Ann Loraine]

Greetings all,

I'm attempting to process some CEL files from an Affymetrix
Arabidopsis tiling array using AffyTiling's AnalyzeTilingCelFiles
function.

How do I tell the function to output the probe x,y coordinates from the array?

So far as I can tell, the x and y coordinates of a probe on the array
grid are the only truly unique identifiers for a probe on any
microarray, and I would like to use these to cross-reference with
other data, such as the probe positions on newer genome versions or
even different genomes from related species.

The function AnalyzeTilingCel Files appears to output the probe
intensity values - one probe per row - but it appears to create a new
identifier for each probe instead of using the x and y coordinates
from the array.

For example, here is an example output row:

"At:TIGRv5;chr1-322"	"322"	"At:TIGRv5;chr1"	"4.43950941028621"	
"2.66476527154283"	"3.52655427353936"	"2.81831265735108"

The first value in the row is meant to be the identifier for the probe
- it uses genomic coordinates to identify the probe.

However, the genomic coordinates are unstable and change from release
to release. It would be very helpful if the output could include the
probe's x and y coordinates from the array instead of this identifier.

Is there any way to do this?

Your help would be much appreciated!

Sincerely,

Ann Loraine
Associate Professor
Dept. of Bioinformatics and Genomics
University of North Carolina, Charlotte

I tried recreating a BPMAP file that references the most up-to-date
version of the genome but