[BioC] Multiple Platforms: Beyond Gene Symbols as Identifiers

[Thomas Hampton]

Marc,

Thanks for your reply.

For a unique gene identifier, do you recommend ENTREZID as over SYMBOL?

I am  comparing three experiments on three platforms

hgu95av2.db
hgu133a
hgu133a + b

So what I am after is a nice common identifier for these chips.

Thanks

Tom
On Apr 30, 2009, at 2:09 PM, Marc Carlson wrote:

> Hi Thomas,
>
> Gene symbols cannot be relied upon to be unique in any case.  They are
> frequently "assigned" to multiple different genes.  I might be better
> able to help you if you were a little bit more specific about what you
> are seeing.  But what you should see is that these two platforms have
> mappings for the subset of the genes that they represent.
>
> So for example hgu133b has a mapping for probeset 229819_at to symbol
> A1BG.  But the hgu133a chip does not have a probe that maps to this  
> gene
> symbol.  So that would be one example (at least) of a difference  and
> there are many more.  There may be some overlap for symbols caused in
> part by the fact that some probesets IDs will measure the same gene  
> and
> also because gene symbols are horrible as identifiers but for the most
> part you should see different symbols on these platforms.
>
>
>   Marc
>
>
>
>
>
> Thomas Hampton wrote:
>> I  merged  probe ids from affy hgu133a and b chips, then looked them
>> up using
>>
>> mget(probelist, hgu133aSYMBOL)
>>
>> Then I tried the same lookup with  hgu133bSYMBOL
>>
>> I expected a difference, since the chips contain fairly unique  
>> symbols.
>>
>> Are symbols unique to A or B known to both?
>>
>>
>> Thanks.
>>
>> Tom
>>
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>