[BioC] Simple annotate question: difference in getSYMBOL and lookUp

[merja matilainen]

Hi!

Can someone explain me the difference in the following attempts to add annotation data my genes (I have a dataset done with Illumina arrays)?

This one works:
> geneSymbol=getSYMBOL(fit2$genes$ID, 'lumiHumanV2')
> fit2$genes=data.frame(fit2$genes, geneSymbol=geneSymbol)

Here I get an error:
> geneEntrez=lookUp(fit2$genes$ID, 'lumiHumanV2', 'ENTREZID')
> fit2$genes=data.frame(fit2$genes, geneEntrezID=geneEntrez)
Error in data.frame(fit2$genes, geneEntrezID = geneEntrez) : 
  arguments imply differing number of rows: 48701, 1

I get the same error if I try to look for example for gene function.

I assume the answer is what type of data structure these two functions return. If I understood the vignette getSYMBOL gives me a vector and lookUp gives me a list. (the help topic says 'Either a vector or a list depending on whether multiple values per input are possible') Unfortunately I am not that familiar with R data structures yet. Could you tell me how I can add to the fit2$genes the entrez result? And perhaps explain why the match to the symbol of the gene is not giving multiple values if description is.

Thanks for your help!

Merja
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