Hi,
 
I am facing a problem i cannot solve myselves, despite everything i
read/know. But i assume the solution is easy for the more knowledgable
folks in BioC/R...
 
This does work:
> library(moe430a.db)
> xxyy <- moe430aSYMBOL
> xxyy
SYMBOL map for chip moe430a (object of class "AnnDbBimap")
 
However, for this to work you need to know the array type of the data
that is analyzed.
 
 
Now i would like to automatically extract the (e.g.) SYMBOL mapping from
an annotation.db, thus by retrieving the array type from the eset.
 
> library(affy)
> eset <- rma(data)
> probeids <- featureNames(eset)
> annotation(eset)
[1] "moe430a"
 
But how can i use this info to properly call the SYMBOL mapping?
 
I tried this:
> arraytype <- annotation(eset)
> arraytype <- paste(arraytype, "db", sep = ".")
> arraytype
[1] "moe430a.db"
> arraytype <- paste("package", arraytype, sep = ":")
> gh <- ls(arraytype)
> gh
 [1] "moe430a"              "moe430a_dbconn"       "moe430a_dbfile"
"moe430a_dbInfo"       "moe430a_dbschema"     "moe430aACCNUM"
"moe430aALIAS2PROBE"   "moe430aCHR"           "moe430aCHRLENGTHS"
"moe430aCHRLOC"       
[11] "moe430aCHRLOCEND"     "moe430aENSEMBL"
"moe430aENSEMBL2PROBE" "moe430aENTREZID"      "moe430aENZYME"
"moe430aENZYME2PROBE"  "moe430aGENENAME"      "moe430aGO"
"moe430aGO2ALLPROBES"  "moe430aGO2PROBE"     
[21] "moe430aMAP"           "moe430aMAPCOUNTS"     "moe430aMGI"
"moe430aMGI2PROBE"     "moe430aORGANISM"      "moe430aPATH"
"moe430aPATH2PROBE"    "moe430aPFAM"          "moe430aPMID"
"moe430aPMID2PROBE"   
[31] "moe430aPROSITE"       "moe430aREFSEQ"        "moe430aSYMBOL"
"moe430aUNIGENE"       "moe430aUNIPROT"
 
> gh[33]
[1] "moe430aSYMBOL"
> 
> symbols <- mget(probeids, gh[33])
Error in mget(probeids, gh[33]) : second argument must be an environment
 
This also doesn't work:
> symbols <- mget(probeids, envir=gh[33])
Error in mget(probeids, envir = gh[33]) : 
  second argument must be an environment
 
My approach thus is the wrong approach to automatically extract mappings
from a annotation.db. 
Since i don't know about any other possibility, i would appreciate if
someone could point me to a working solution.
 
Thanks,
Guido  
 

------------------------------------------------ 
Guido Hooiveld, PhD 
Nutrition, Metabolism & Genomics Group 
Division of Human Nutrition 
Wageningen University 
Biotechnion, Bomenweg 2 
NL-6703 HD Wageningen 
the Netherlands 
tel: (+)31 317 485788 
fax: (+)31 317 483342 
internet:   http://nutrigene.4t.com <http://nutrigene.4t.com/>  
email:      guido.hooiveld@wur.nl 



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