Thanks for the replies.  My intent was to map from human to human, and for
my purposes, using the Entrez ID as the common link as suggested in the
replies is fine.  However, I was also curious to if there was a package that
would go beyond using the Entrez IDs to the level of sequence similarity
between probe set IDs, etc.
Thanks,
Andrew

On Fri, Apr 24, 2009 at 12:55 PM, Marc Carlson <mcarlson@fhcrc.org> wrote:

> Hi Andrew,
>
> I am really unsure about why you would want to do this, but if you did,
> you could grab the annotation packages for those two platforms and do
> something like this:
>
> library(hgu95av2.db)
> library(hgu133a.db)
>
> ##just to grab some real probesets for our example
> keys = Lkeys(hgu95av2ENTREZID)[100:200]
>
> ##now lets map 'em
> ##1st step is to get the entrez gene ID (which all of the human packages
> use as a central ID)
> EGs = mget(as.character(keys), hgu95av2ENTREZID, ifnotfound = NA)
>
> ##Then use the other package to the probes that go with those entrez
> gene IDs
> otherProbes = mget(as.character(EGs), revmap(hgu133aENTREZID),
> ifnotfound = NA)
>
> For this example I have assumed that you are trying to map between
> platforms of the same species.  For different species that problem
> becomes a lot more challenging.
>
>
>  Marc
>
>
>
>
> Andrew Yee wrote:
> > This is a naive question, but is there a Bioconductor package that will
> map
> > probe set ids from one chip to another chip?
> > Thanks,
> > Andrew
> >
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> >
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> >
>
>

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