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