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Hi Yanqin, Regarding getting physical locations for each probe of the probeset, you can try something like: indices<-indexProbes(affyBatch,"pm",probeset.id) where probeset.id is a vector of probeset IDs to get indices corresponding to your probesets of interest. This returns a named list, named according a probeset id. locations<-indices2xy(unlist(indices),abatch=affyBatch) This gives a set of x and y coordinates for each probe of each probeset you specified in probeset.id That should work. Hope that helps, Duane Hassane -----Original Message----- From: bioconductor-bounces@stat.math.ethz.ch [mailto:bioconductor-bounces at stat.math.ethz.ch]On Behalf Of Yanqin Yang Sent: Thursday, August 03, 2006 12:02 PM To: bioconductor at stat.math.ethz.ch Subject: [BioC] how to get affy probe set physical location on the chip? Hello, I have a set of rat affymetrix array. One of chip shows there is bright 'blue' corner in the 'sign.resids' image after applied 'affyPLM' package. How could I retrieve the affy ID corresponding the 'blue' area? Or, if I have a set of affy IDs, how could I get their physical location on the array? Thanks a lot! Yanqin --------------------------------- [[alternative HTML version deleted]] _______________________________________________ Bioconductor mailing list Bioconductor at stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor