[BioC] hgu133plus2cdf

[Kasper Daniel Hansen]

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
>
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