[BioC] from rat codelink to human locuslink

[Weiwei Shi]

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?)

thanks,

weiwei


On 11/2/06, Sean Davis <sdavis2 at mail.nih.gov> wrote:
> Weiwei Shi wrote:
> > hi,
> >
> > I am wondering if bioconductor can help me do some conversion from rat
> > codelink probe id's to human locuslink id's?
> >
> > A further, more general question is, is there some package which can
> > handle this kind of conversion between different id systems and
> > different species?
> >
> You will probably need to convert your codelink probe IDs to some useful
> public ID.  I don't know what codelink supplies as a mapping for their
> probe IDs.  However, you can then probably use the biomart package for a
> general conversion between different id systems in different species.
>
> Sean
>


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

"Did you always know?"
"No, I did not. But I believed..."
---Matrix III