[BioC] Question about ATH1 array

[Wolfgang Huber]

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 at salk.edu
>
> _______________________________________________
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> 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