Hi Wolfgang, Thanks for your reply, that clears my confusion. > getOption("BioC")$affy$xy.offset [1] 1 Does this mean that the xy-coordinates for the features on Affymetrix chips were decided to start at 1, while xy-coordinates in ath1121501probe starts at 0. So I can either set the offset to 0 or add 1 to xy-coordinates on ath1121501probe profile. Please indicate if I am wrong. I met similar problem before, but with self-made probe file. Thought Affy's CEL and Probe should be consistent with each other. Fangxin > Hi Fanqxin, > > Please read the documentation, i.e. the help page for indices2xy. > The problem is whether you start couting at 0 or 1. Unfortunately, both > ways have been used in different places! > > What do you get when you say: > > getOption("BioC")$affy$xy.offset > > > Best wishes > Wolfgang > > <quote who="Fangxin Hong"> >> Hi list; >> I have been working on ATH1 array for a while, and found that the xypos >> from (1) .CEL file with function indexProbes and indices2xy, (2) >> ath1121501probe do not match with each other. It seems that each >> coordinate differ by 1 >> Any idea? >> >> Thanks a lot. >> Fangxin >> >>> library(ath1121501probe) >>> probe=data.frame(ath1121501probe) >>> index=which(probe[,4]=="257615_at") >>> probe[index,2:4] >> x y Probe.Set.Name >> 139793 107 443 257615_at >> 139794 297 79 257615_at >> 139795 131 235 257615_at >> 139796 543 221 257615_at >> 139797 593 87 257615_at >> 139798 616 267 257615_at >> 139799 293 147 257615_at >> 139800 337 191 257615_at >> 139801 298 103 257615_at >> 139802 234 515 257615_at >> 139803 603 439 257615_at >> >>> pm.i <- indexProbes(Ath1.batch, which="pm", genenames="257615_at")[[1]] >>> pm.i.xy <- indices2xy(pm.i, abatch = Ath1.batch) >>> pm.i.xy >> x y >> [1,] 108 444 >> [2,] 298 80 >> [3,] 132 236 >> [4,] 544 222 >> [5,] 594 88 >> [6,] 617 268 >> [7,] 294 148 >> [8,] 338 192 >> [9,] 299 104 >> [10,] 235 516 >> [11,] 604 440 >> >> >> -- >> Fangxin Hong, Ph.D. >> Plant Biology Laboratory >> The Salk Institute >> 10010 N. Torrey Pines Rd. >> La Jolla, CA 92037 >> E-mail: fhong@salk.edu >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor@stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> > > > ------------------------------------- > Wolfgang Huber > European Bioinformatics Institute > European Molecular Biology Laboratory > Cambridge CB10 1SD > England > Phone: +44 1223 494642 > Http: www.ebi.ac.uk/huber > ------------------------------------- > > -- Fangxin Hong, Ph.D. Plant Biology Laboratory The Salk Institute 10010 N. Torrey Pines Rd. La Jolla, CA 92037 E-mail: fhong@salk.edu