Thanks for your help.  And I should have looked at the entry on NCBI more
carefully for the aliases of NOL3.
In the future, I should just use the revmap() to restrict the query to
official symbols.

mget("MYC", env=revmap(u133x3pSYMBOL))

Thanks,
Andrew


On Mon, Jan 26, 2009 at 7:29 PM, Marc Carlson <mcarlson@fhcrc.org> wrote:

> Hi Andrew,
>
> I think that what is confusing you is that the "alias" and "symbol"
> mappings have different meanings.  The "alias" mapping is for mapping
> all possible gene symbols (as used by scientists) and the "symbol"
> mapping only returns one (the "official" one according to NCBI) symbol
> per probeset.
>
> If you were to look at the reverse map of the alias map, you could see
> this demonstrated here:
>
> mget("4854714C_3p_s_at", env=revmap(u133x3pALIAS2PROBE))
>
> This returns all the symbols associated with this probeset including the
> "official" one  of NOL3:
> $`4854714C_3p_s_at`
> [1] "ARC"   "CARD2" "MYC"   "MYP"   "NOL3"  "NOP"   "NOP30"
>
> In contrast, the u133x3pSYMBOL mapping only maps to the "official" gene
> symbol for a probeset, so all you get there is NOL3.
>
>
>  Marc
>
>
>
> Andrew Yee wrote:
> > I was trying to figure out why I was getting this output with the
> u133x3p.db
> > package.
> >
> > Specifically, if I enter:
> >
> > mget("MYC", env=u133x3pALIAS2PROBE)
> >
> > It returns:
> >
> > $MYC
> > [1] "4854714C_3p_s_at"      "Hs.300470.0.A1_3p_at"
>  "Hs2.372887.1.S1_3p_at"
> > "g12962934_3p_a_at"     "g3126906_3p_a_at"
> >
> > However, if you try to convert the first probe set ID returned,
> >
> > mget( "4854714C_3p_s_at", env=u133x3pSYMBOL)
> >
> > it returns:
> >
> > $`4854714C_3p_s_at`
> > [1] "NOL3"
> >
> > I'm puzzled why the output from u133x3pALIAS2PROBE doesn't exactly match
> up
> > with u133x3pSYMBOL
> >
> > Thanks,
> > Andrew
> >
> >       [[alternative HTML version deleted]]
> >
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> >
> >
>
>

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