[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.
> > 
> > _______________________________________________
> > Bioconductor mailing list
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> > http://news.gmane.org/gmane.science.biology.informatics.conductor
> 
> --
> 
> 
> 

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