[BioC] confused about mget with u133x3p.db and u133x3pALIAS2PROBE

[Marc Carlson]

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]]
>
> _______________________________________________
> 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
>
>