[BioC] probe level annotation
Shi, Tao
shidaxia at yahoo.com
Mon Oct 2 23:08:13 CEST 2006
Hi Holger,
If that's the case, how do you match them up? Thanks,
...Tao
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Hi Tao,
at least for the Plus2 and the X3P chip, the order of hgu133plus2probe and pm(...) slightly differ.
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
>
> >
>
> > _______________________________________________
>
> > Bioconductor mailing list
>
> > Bioconductor at stat.math.ethz.ch
>
> > https://stat.ethz.ch/mailman/listinfo/bioconductor
>
> > Search the archives:
> http://news.gmane.org/gmane.science.biology.informatics.conductor
>
>
>
>
>
> --
>
> 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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>
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