[BioC] Bioconductor package to map probe set ids from one chip to another chip

[Marc Carlson]

Hi Andrew,

The probe packages will furnish you with the actual sequences of the
probes from the array platforms.

  Marc



Andrew Yee wrote:
> 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 at fhcrc.org
> <mailto:mcarlson at 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
>     >
>     >       [[alternative HTML version deleted]]
>     >
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