On Mon, May 17, 2010 at 4:45 AM, Taylor, Katie <kt70@leicester.ac.uk> wrote:

> 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.
>
>
Hi, Katie.

You'll need to provide the code that produced probeids or at least some
information about what is in probeids (summary(probeids), head(probeids),
class(probeids), as examples).  Also, you absolutely need to include
sessionInfo() for every email to the list for your question to be adequately
answered.

Sean

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