[BioC] probe level annotation

[Shi, Tao]

Hi Jim,

Thanks!  My bad.  I accidentally selected the HT 133A array.

Any idea on my second question?  I assume they are listed in the same order, but not sure whether it's right.

...Tao




----- Original Message ----
From: James W. MacDonald <jmacdon at med.umich.edu>
To: "Shi, Tao" <shidaxia at yahoo.com>
Cc: bioconductor at stat.math.ethz.ch
Sent: Monday, October 2, 2006 1:36:35 PM
Subject: Re: [BioC] probe level annotation

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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