[BioC] Multiple Platforms: Beyond Gene Symbols as Identifiers

Marc Carlson mcarlson at fhcrc.org
Thu Apr 30 22:38:46 CEST 2009


Hi Thomas,

Entrez Gene IDs are a great alternative to symbols.  They are not
recycled.  So if you meet the same entrez ID in another setting  you can
be assured that it refers to the same thing that it did before.  In
contrast, with gene symbols you have cases like the "VH" gene which is
presently assigned to 36 different genes in humans!  So if someone tells
you that they work on the VH gene you have to ask them which one??? 
That sort of nonsense is just not helpful when doing informatics work.

So yes, you should probably use Entrez Gene IDs.


  Marc




Thomas Hampton wrote:
> 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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>>
>
>



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