[BioC] from rat codelink to human locuslink

[Diego Diez]

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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