[BioC] from rat codelink to human locuslink

[Weiwei Shi]

yes, that's why i was confused b/c i checked some codelink and they
start with GE. But i used that package and put the unigene id the data
provides; some are recognized by biomaRt while some are not.
I will try tomorrow (it is too late for today :(

weiwei

On 11/2/06, Diego Diez <diez at kuicr.kyoto-u.ac.jp> wrote:
> On Thu, 2 Nov 2006, Sean Davis wrote:
>
> > Weiwei Shi wrote:
> > > Hi,
> > >
> > > I have 3 examples like this:
> > > Probe_ID        UniGene_ID      UniGene_Name
> > > AA799301_PROBE1 Rn.107913       Lgtn protein (DBSS)
> > > AA799313_PROBE1 Rn.32316        "sialyltransferase 10
> > > (alpha-2,3-sialyltransferase VI)"
> > > AA799329_PROBE1 Rn.112856       RIKEN cDNA 4632417K18 (Mm.) (DBSS)
> > >
> > > I think the UniGene_ID might work for the purpose of using biomartRt
> > > package (is it what you meant by biomart?). But the thing is, I look
> > > through the package intro but I did not find how to convert between
> > > species. Should I choose dataset for rat first, and then use rat2human
> > > conversion (i have a local program to do that but I am curious how
> > > biomartRt or other packages in R do this?)
> > Hi, Weiwei.  You'll probably want to look at the help pages for biomaRt
> > (note the correct capitalization--sorry for the confusion).  To see a
> > list of help pages, you can use the simple command:
> >
> >  > help(package=biomaRt)
> >
> > There are a couple of functions that look promising: getXref and
> > getHomolog.  You might want to look into those a bit.
> >
> > As for your probe ID's, it looks like they are a concatenation of a
> > Genbank accession number and "PROBE1", so those could be useful.
> > Unigene ID could also potentially be useful, but that depends a bit on
> > how old the annotation is, as Unigene IDs change and are deleted on a
> > regular basis as part of each new unigene build.
>
> Actually, those probe ID's are not the currently used Codelink probe ID's
> but the LEGACY_PROBE_NAME. The annotation packages found in Bioconductor
> dont use this probe ids so they cannot be used to map to public
> identifiers.  I wonder if it is also available the CUSTUMER_PROBE_NAME,
> which has the form GExxxxx (x being numbers, like GE12209) and is the
> identifier used by Codelink.
>
> D.
>
> >
> > Sean
> >
> > _______________________________________________
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> > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
> >
>
>


-- 
Weiwei Shi, Ph.D
Research Scientist
GeneGO, Inc.

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