[BioC] hgu133plus2cdf

[James W. MacDonald]

jsv at stat.ohio-state.edu wrote:
> I'm having trouble getting symbols for this chip.  I've loaded the
> hgu133plus2cdf package:

The problem arises from the fact that you are loading and using the 
hgu133plus2cdf package rather than the hgu133plus2 package, which is 
what you want.

Best,

Jim


> 
> 
>>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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-- 
James W. MacDonald
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623