[BioC] help with annaffy package

[Taylor, Katie]

Hello,

I hope this email finds you well. I am trying to annotate annaffy data and i'm running into some problems. One problem that I faced last week was fixed with your help and I am hoping that you will know what to do with my current problem. I have copied the R output below with the waring messages that I am getting.

 library(annaffy)
Loading required package: GO.db
Loading required package: AnnotationDbi
Loading required package: DBI
Loading required package: KEGG.db
> aaf.handler()
 [1] "Probe"               "Symbol"              "Description"        
 [4] "Chromosome"          "Chromosome Location" "GenBank"            
 [7] "Gene"                "Cytoband"            "UniGene"            
[10] "PubMed"              "Gene Ontology"       "Pathway"            
> anncols <- aaf.handler()[c(1:4, 7, 10)]
> anntable <- aafTableAnn(probeids[1:100], "hgu133plus2.db",
+ anncols)
Loading required package: hgu133plus2.db
Loading required package: org.Hs.eg.db
Error in probeids[1:100] : object of type 'closure' is not subsettable
Error in as.list(probeids) : 
  error in evaluating the argument 'x' in selecting a method for function 'as.list'
> anntable <- aafTableAnn(probeids[1:54676], "hgu133plus2.db",
+ anncols)
Error in probeids[1:54676] : object of type 'closure' is not subsettable
Error in as.list(probeids) : 
  error in evaluating the argument 'x' in selecting a method for function 'as.list'
> 
I don't know what to do with the probids. Any help that you give me would be greatly appreciated.

Best Wishes,

Katie