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

[Hervé Pagès]

Hi Andrew,

I've just added an example in the Biostrings package (v 2.13.2, that's
in devel) to show how it can be used to map probe set IDs between chips,
based on probe comparisons.
For example it takes about 15 minutes to build the complete mapping
between hgu95av2 and hgu133a (201800 and 247965 probes, respectively).

See '?vwhichPDict' (example G.) and let me know if you have questions.

Cheers,
H.


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> 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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> 
> 	[[alternative HTML version deleted]]
> 
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-- 
Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
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