[BioC] Question about ATH1 array

[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