Hello, 

I want obtain groups of genes (for association genes with the phenotype), to be built from Gene Ontology. I used this script:

> arraysdc.rma.gsc = GeneSetCollection(arraysdc.rma, setType = GOCollection())

And R said me:

Error in as.list(getAnnMap("GO2PROBE", annotation(idType))) : 
  error in evaluating the argument 'x' in selecting a method for function 'as.list': Error in (function (classes, fdef, mtable)  : 
  unable to find an inherited method for function ‘columns’ for signature ‘"AffyGenePDInfo"’

The arrays that I used are Human Gene 2.0 ST.

Thank you very much for the help, 

Santi.

Try this.

annotation(arraysdc.rma) <- "hugene20sttranscriptcluster.db"

and then run GeneSetCollection() again. The problem arises because oligo sets the annotation slot to be the pdInfoPackage used to map probes to probesets, rather than the annotation package that maps probesets to gene-based information.