Question about ATH1 array
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Fangxin Hong ▴ 810
@fangxin-hong-912
Last seen 9.6 years ago
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
probe probe • 758 views
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@wolfgang-huber-3550
Last seen 3 months ago
EMBL European Molecular Biology Laborat…
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
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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
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@rhonda-decook-1033
Last seen 9.6 years ago
Fangxin, I believe if you choose the option "xy.offset=0" in the 'indices2xy' function you'll get the indices you're looking for. I was off by 1 in my initial exploration and this option (which can be set to 0 or 1) corrected the disagreement. ## For example, I used this for my affybatch called 'cel.files': indices2xy(95115,abatch=cel.files,xy.offset=0) xy2indices(418,133,abatch=cel.files,xy.offset=0) Rhonda > 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 >
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