[BioC] Question about ATH1 array

[Fangxin Hong]

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 at salk.edu
>>
>> _______________________________________________
>> Bioconductor mailing list
>> Bioconductor at 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 at salk.edu