[BioC] probe level annotation

[James W. MacDonald]

Hi Tao,

I just checked netaffx, and I get the same as the hgu133aprobe and 
hgu133acdf show:

CACCCAGCTGGTCCTGTGGATGGGA  	467  	181  	3330  	Antisense
GCCCCACTGGACAACACTGATTCCT 	531 	299 	3443 	Antisense
TGGACCCCACTGGCTGAGAATCTGG 	86 	557 	3512 	Antisense
AAATGTTTCCTTGTGCCTGCTCCTG 	365 	115 	3563 	Antisense
TCCTTGTGCCTGCTCCTGTACTTGT 	207 	605 	3570 	Antisense
TGCCTGCTCCTGTACTTGTCCTCAG 	593 	599 	3576 	Antisense
TCCTGTACTTGTCCTCAGCTTGGGC 	425 	607 	3583 	Antisense
ACTTGTCCTCAGCTTGGGCTTCTTC 	552 	101 	3589 	Antisense
TCCTCCATCACCTGAAACACTGGAC 	680 	607 	3615 	Antisense
AAGCCTATACGTTTCTGTGGAGTAA 	532 	139 	3713 	Antisense
TTGGACATCTCTAGTGTAGCTGCCA 	143 	709 	3786 	Antisense
TCTCTAGTGTAGCTGCCACATTGAT 	285 	623 	3793 	Antisense
GTGTAGCTGCCACATTGATTTTTCT 	383 	479 	3799 	Antisense
GCCACATTGATTTTTCTATAATCAC 	129 	279 	3807 	Antisense
TACACTAATATATGGACCTAGCTTG 	62 	651 	3871 	Antisense
ATATATGGACCTAGCTTGAGGCAAT 	308 	15 	3878 	Antisense

No idea why you got something different.

Best,

Jim





Shi, Tao wrote:
> 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
> 
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-- 
James W. MacDonald, M.S.
Biostatistician
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623


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