[BioC] hgu133plus2cdf

jsv@stat.ohio-state.edu jsv at stat.ohio-state.edu
Tue Jan 31 05:18:55 CET 2006

I'm having trouble getting symbols for this chip.  I've loaded the
hgu133plus2cdf package:

> sessionInfo()
R version 2.2.0, 2005-10-06, i386-pc-mingw32

attached base packages:
[1] "tools"     "methods"   "stats"     "graphics"  "grDevices" "utils"   
[8] "base"

other attached packages:
      hgu95av2        annaffy           KEGG             GO hgu133plus2cdf
      "1.10.0"        "1.2.0"       "1.10.0"       "1.10.0"       "1.10.0"

The problem comes when I try

> g.symbols <- aafSymbol(gn,"hgu133plus2cdf")
Error in mget(c("1007_s_at", "1053_at", "117_at", "121_at", "1255_g_at",  :
        object "hgu133plus2cdfSYMBOL" not found

The package has the following objects:

> objects("package:hgu133plus2cdf")
[1] "hgu133plus2cdf" "i2xy"           "xy2i"

This seems particularly sparse, compared to, say,

 [1] "hgu95av2"             "hgu95av2ACCNUM"       "hgu95av2CHR"         
 [5] "hgu95av2CHRLOC"       "hgu95av2ENZYME"       "hgu95av2ENZYME2PROBE"
 [9] "hgu95av2GO"           "hgu95av2GO2ALLPROBES" "hgu95av2GO2PROBE"    
[13] "hgu95av2MAP"          "hgu95av2MAPCOUNTS"    "hgu95av2OMIM"        
[17] "hgu95av2PATH"         "hgu95av2PATH2PROBE"   "hgu95av2PFAM"        
[21] "hgu95av2PMID2PROBE"   "hgu95av2PROSITE"      "hgu95av2QC"          
[25] "hgu95av2REFSEQ"       "hgu95av2SUMFUNC"      "hgu95av2SYMBOL"      


g.symbols <- aafSymbol(gn,"hgu95av2")

finds about 300 gene symbols using the older probe identifiers.

Any help on finding and loading the latest version of hgu133plus2cdf onto
a Windows XP system, or finding some other way to get the symbols would be
much appreciated.

Joe Verducci

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