[BioC] probe level annotation

[Shi, Tao]

Hi list,

I found the XY coordinates for the probes in 'hgu133aprobe' are not exactly the same as those shown on NetAffx.com.  Please see below.

Also, is the order of the probes from pm(myAffyData, '1007_s_at'), for examples, the same as in 'hgu133aprobe'? 

thanks,

...Tao


> R.Version()
$platform
[1] "i386-pc-mingw32"

$arch
[1] "i386"

$os
[1] "mingw32"

$system
[1] "i386, mingw32"

$status
[1] ""

$major
[1] "2"

$minor
[1] "3.0"

$year
[1] "2006"

$month
[1] "04"

$day
[1] "24"

$`svn rev`
[1] "37909"

$language
[1] "R"

$version.string
[1] "Version 2.3.0 (2006-04-24)"

> library(hgu133aprobe)
> data(hgu133aprobe)
> as.data.frame(hgu133aprobe[1:16,])
                    sequence   x   y Probe.Set.Name Probe.Interrogation.Position Target.Strandedness
1  CACCCAGCTGGTCCTGTGGATGGGA 467 181      1007_s_at                         3330           Antisense
2  GCCCCACTGGACAACACTGATTCCT 531 299      1007_s_at                         3443           Antisense
3  TGGACCCCACTGGCTGAGAATCTGG  86 557      1007_s_at                         3512           Antisense
4  AAATGTTTCCTTGTGCCTGCTCCTG 365 115      1007_s_at                         3563           Antisense
5  TCCTTGTGCCTGCTCCTGTACTTGT 207 605      1007_s_at                         3570           Antisense
6  TGCCTGCTCCTGTACTTGTCCTCAG 593 599      1007_s_at                         3576           Antisense
7  TCCTGTACTTGTCCTCAGCTTGGGC 425 607      1007_s_at                         3583           Antisense
8  ACTTGTCCTCAGCTTGGGCTTCTTC 552 101      1007_s_at                         3589           Antisense
9  TCCTCCATCACCTGAAACACTGGAC 680 607      1007_s_at                         3615           Antisense
10 AAGCCTATACGTTTCTGTGGAGTAA 532 139      1007_s_at                         3713           Antisense
11 TTGGACATCTCTAGTGTAGCTGCCA 143 709      1007_s_at                         3786           Antisense
12 TCTCTAGTGTAGCTGCCACATTGAT 285 623      1007_s_at                         3793           Antisense
13 GTGTAGCTGCCACATTGATTTTTCT 383 479      1007_s_at                         3799           Antisense
14 GCCACATTGATTTTTCTATAATCAC 129 279      1007_s_at                         3807           Antisense
15 TACACTAATATATGGACCTAGCTTG  62 651      1007_s_at                         3871           Antisense
16 ATATATGGACCTAGCTTGAGGCAAT 308  15      1007_s_at                         3878           Antisense
> package.version('hgu133aprobe')
[1] "1.12.0"


And from NetAffx.com

Probe Sequence(5'-3')        Probe X        Probe Y        Probe Interrogation
Position     Target Strandedness
CACCCAGCTGGTCCTGTGGATGGGA     197     207     3330     Antisense
GCCCCACTGGACAACACTGATTCCT     592     319     3443     Antisense
TGGACCCCACTGGCTGAGAATCTGG     85     591     3512     Antisense
AAATGTTTCCTTGTGCCTGCTCCTG     559     139     3563     Antisense
TCCTTGTGCCTGCTCCTGTACTTGT     269     633     3570     Antisense
TGCCTGCTCCTGTACTTGTCCTCAG     378     629     3576     Antisense
TCCTGTACTTGTCCTCAGCTTGGGC     536     643     3583     Antisense
ACTTGTCCTCAGCTTGGGCTTCTTC     479     125     3589     Antisense
TCCTCCATCACCTGAAACACTGGAC     575     643     3615     Antisense
AAGCCTATACGTTTCTGTGGAGTAA     497     161     3713     Antisense
TTGGACATCTCTAGTGTAGCTGCCA     635     739     3786     Antisense
TCTCTAGTGTAGCTGCCACATTGAT     74     659     3793     Antisense
GTGTAGCTGCCACATTGATTTTTCT     660     503     3799     Antisense
GCCACATTGATTTTTCTATAATCAC     80     313     3807     Antisense
TACACTAATATATGGACCTAGCTTG     739     685     3871     Antisense
ATATATGGACCTAGCTTGAGGCAAT     242     31     3878     Antisense