[BioC] Difference between hgu133a.db and hgu133b.db

[Marc Carlson]

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
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives:
> http://news.gmane.org/gmane.science.biology.informatics.conductor
>