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

[Marc Carlson]

One more thing,

I feel that I have to add an additional comment here.  And that is to
PLEASE be careful (with whatever it is that you have planned).  In many
cases the probesets in question may have been made to measure a
completely different transcript on one platform than on another.  So
while we can definitely join them via their association with a
particular gene in the way that I have shown you here, you could end up
interpreting things very badly if you don't pay very careful attention
to what they are actually meant to be sticking to.

  Marc



Marc Carlson 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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>>     
>
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