[BioC] probe level annotation
Holger Schwender
holger.schw at gmx.de
Mon Oct 2 23:32:54 CEST 2006
Hi Tao,
using the x and the y coordinates in the annotation file, i.e., e.g., hgu133plus2probe$x and hgu133plus2probe$y, and the functions xy2indices and pmindex.
Let tmp be an Affybatch object, and NR the number of rows on the chip (for the Plus2 chip, NR=1,164). Then something like
> pI<-unlist(pmindex(tmp))
> mat.xy<-cbind(x=hgu133plus2probe$x,y=hgu133plus2probe$y)
> ids.probes<-xy2indices(mat.xy,nr=NR)
> match(ids.probes,pI)
should work.
Best,
Holger
-------- Original-Nachricht --------
Datum: Mon, 2 Oct 2006 14:08:13 -0700 (PDT)
Von: "Shi, Tao" <shidaxia at yahoo.com>
An: bioconductor at stat.math.ethz.ch
Betreff: probe level annotation
> 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
> >
> >
> >
> >
> >
> > **********************************************************
> >
> > Electronic Mail is not secure, may not be read every day, and should not
> > be used for urgent or sensitive issues.
> >
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>
> --
>
>
>
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