[BioC] hgu133plus2 GO issues

[Jake]

Hi list,

Could someone please help me understand the differences between the
(hgu133plus2)GO, GO2PROBE, GO2ALLPROBES?  I've found discepancies that I
can't quite explain:

 > mget("GO:0042611", hgu133plus2GO2PROBE)
Error: value for 'GO:0042611' not found

> mget("GO:0042611", hgu133plus2GO2ALLPROBES)
$"GO:0042611"
          <NA>            IEA            IEA            IEA
<NA>
   "209309_at"  "217014_s_at"    "210325_at"  "218831_s_at"
"1553402_a_at"
          <NA>           <NA>           <NA>           <NA>
<NA>
 "206086_x_at"  "206087_x_at"  "210864_x_at"  "211326_x_at"
"211327_x_at"
          <NA>           <NA>           <NA>           <NA>
<NA>
 "211328_x_at"  "211329_x_at"  "211330_s_at"  "211331_x_at"
"211332_x_at"
          <NA>           <NA>           <NA>            IEA
<NA>
 "211863_x_at"  "211866_x_at"  "214647_s_at"    "235754_at"
"213932_x_at"
           IEA           <NA>           <NA>            IEA
<NA>
 "215313_x_at"  "208729_x_at"  "209140_x_at"  "211911_x_at"
"208812_x_at"
          <NA>           <NA>            IEA           <NA>
<NA>
 "211799_x_at"  "214459_x_at"  "216526_x_at"    "200904_at"
"200905_x_at"
           IEA           <NA>           <NA>            IEA
<NA>
 "217456_x_at"  "204806_x_at"  "221875_x_at"    "221978_at"
"210514_x_at"
          <NA>           <NA>           <NA>            IEA
IEA
 "211528_x_at"  "211529_x_at"  "211530_x_at"  "217436_x_at"
"231748_at"
          <NA>            IEA            IEA            IEA
   "221291_at"    "238542_at"    "221323_at" "1552777_a_at"

and finally...

### "208729_x_at" is one of the probes returned with the above command
> grep("GO:0042611",unlist(mget("208729_x_at", hgu133plus2GO)))
numeric(0)



"208729_x_at" is on the hgu133plus2 chip, but GO and GO2ALLPROBES don't
map it to the same GO ID.

Is there something wrong here or am I just missing something?  If
different, which is the most "reliable" mapping?  I'm concerned because
I went through to validate GO IDs I had gotten from the GOHyperG
function (a total of 314), and 117 of those I could not map back to my
significant probe list using the hgu133plus2GO annotation.  I noticed by
looking at the GOHyperG function that it uses information from
GO2ALLPROBES.

Any help/enlightenment is much appreciated.

PS - using R 2.2.1 with hgu133plus2 1.10.0

--Jake