[BioC] hgu133plus2cdf

[Joseph S. Verducci]

Thanks to James and Kasper for pointing out the distinction between 
the cdf and annotation packages. 

Joe

_______________________

On Tue, 2006-01-31 at 10:06 -0800, Kasper Daniel Hansen wrote:
> You are confusing an annotation package with a cdf package. The  
> annotation package contains all the symbols, where the cdf package  
> contains information about which probes are PM/MM and how they are  
> bundled together in probesets (probing genes).
> 
> Use hgu133plus2 instead, and just for the sake of it, compare  
> hgu133plus with hgu95av2 and hgu133plus2cdf with hgu95av2cdf
> 
> There is a third kind of package, the probe package  
> (hgu133plus2probe) containing information on the actual sequences  
> synthezised on the array.
> 
> /Kasper
> 
> 
> 
> On Jan 30, 2006, at 8:18 PM, jsv at stat.ohio-state.edu wrote:
> 
> > 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"
> >  "datasets"
> > [8] "base"
> >
> > other attached packages:
> >       hgu95av2        annaffy           KEGG             GO  
> > hgu133plus2cdf
> >           affy
> >       "1.10.0"        "1.2.0"       "1.10.0"       "1.10.0"        
> > "1.10.0"
> >        "1.8.1"
> >        Biobase
> >        "1.8.0"
> >
> > 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,
> >
> >  objects("package:hgu95av2")
> >  [1] "hgu95av2"             "hgu95av2ACCNUM"       "hgu95av2CHR"
> > "hgu95av2CHRLENGTHS"
> >  [5] "hgu95av2CHRLOC"       "hgu95av2ENZYME"        
> > "hgu95av2ENZYME2PROBE"
> > "hgu95av2GENENAME"
> >  [9] "hgu95av2GO"           "hgu95av2GO2ALLPROBES" "hgu95av2GO2PROBE"
> > "hgu95av2LOCUSID"
> > [13] "hgu95av2MAP"          "hgu95av2MAPCOUNTS"    "hgu95av2OMIM"
> > "hgu95av2ORGANISM"
> > [17] "hgu95av2PATH"         "hgu95av2PATH2PROBE"   "hgu95av2PFAM"
> > "hgu95av2PMID"
> > [21] "hgu95av2PMID2PROBE"   "hgu95av2PROSITE"      "hgu95av2QC"
> > "hgu95av2QCDATA"
> > [25] "hgu95av2REFSEQ"       "hgu95av2SUMFUNC"      "hgu95av2SYMBOL"
> > "hgu95av2UNIGENE"
> >
> >
> > Interestingly,
> >
> > 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
> >
> > _______________________________________________
> > Bioconductor mailing list
> > Bioconductor at stat.math.ethz.ch
> > https://stat.ethz.ch/mailman/listinfo/bioconductor
> 
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-- 
Joseph S. Verducci <jsv at stat.ohio-state.edu>