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

[Marc Carlson]

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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