[BioC] probe level annotation
James W. MacDonald
jmacdon at med.umich.edu
Mon Oct 2 23:04:33 CEST 2006
Holger Schwender wrote:
> Hi Tao,
>
> at least for the Plus2 and the X3P chip, the order of hgu133plus2probe and pm(...) slightly differ.
It depends on what we get from Affy. The probe packages are based on the
Affymetrix XXX_probe_tab files, which list things out a particular
order, and the cdfs are based on the cdf files. If Affy happened to list
things out in the same order for both input files, then things will line
up. If not, then they won't ;-D
As Holger says, these two are slightly different. I wouldn't be
surprised if that were true for all the chips (and I wouldn't be
surprised if some were 100% consistent either...).
Best,
Jim
>
> Best,
> Holger
>
>
> -------- Original-Nachricht --------
> Datum: Mon, 2 Oct 2006 13:53:00 -0700 (PDT)
> Von: "Shi, Tao" <shidaxia at yahoo.com>
> An: "James W. MacDonald" <jmacdon at med.umich.edu>
> Betreff: Re: [BioC] probe level annotation
>
>
>>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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>>
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>>
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>>
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>>
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>>
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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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>
>
--
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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