[BioC] OntoCompare Error

[Johannes Graumann]

Paquet, Agnes wrote:

> OntoCompare will only work with the following probe types: Gene Ontology
> ids, Affymetrix oligo Ids and Operon human and Mouse oligo ids. Other
> types will not be recognized and you will get an error.
Thanks so much for this clarification, but now I isolated all the GO terms
for my data set and fed a list (14000 or so) of them to the function
in 'result <- OntoCompare(list,probeType = "GO")' fashion and this results
in a similar error:

> GOs
...
[14291] "GO:0003677" "GO:0004386" "GO:0005524" "GO:0016787" "GO:0001882"
[14296] "GO:0003779" "GO:0005509" "GO:0005515" "GO:0042803" "GO:0051015"
[14301] "GO:0003677" "GO:0003700" "GO:0005515" "GO:0008270" "GO:0043565"
[14306] "GO:0046872" "GO:0000166" "GO:0003774" "GO:0003779" "GO:0005515"
[14311] "GO:0005516" "GO:0005524" "GO:0005515" "GO:0046982" "GO:0003677"
[14316] "GO:0004090" "GO:0016491" "GO:0000146" "GO:0000166" "GO:0003774"
[14321] "GO:0003779" "GO:0005515" "GO:0005516" "GO:0005524" "GO:0016787"
[14326] "GO:0016887" "GO:0030898" "GO:0042803" "GO:0043495" "GO:0043531"
[14331] "GO:0051015" "GO:0003676" "GO:0008270" "GO:0046872" "GO:0005488"
[14336] "GO:0005515" "GO:0008565"
> result <- ontoCompare(GOs,probeType = "GO")
[1] "Starting ontoCompare..."
Error in as.vector(x, mode) : invalid argument 'mode'

Am I still not getting this tool?

Joh

>  
> Best,
>  
> Agnes
> 
> ________________________________
> 
> From:
> bioconductor-bounces at stat.math.ethz.ch on
> behalf of Johannes Graumann Sent: Fri 2/23/2007 8:05 AM To:
> bioconductor at stat.math.ethz.ch Subject:
> [BioC] OntoCompare Error
> 
> 
> 
> Hello,
> 
> With the help of this list I succeeded in creating an annotation package
> using ABPkgBuilder/AnnBuilder ("Mus.musculus.GoMap.20070223"), which
> installs fine.
> I then tried to run goTools' ontoCompare function like this:
> 
> result <- ontoCompare(ProtNames, probeType =
> "Mus.musculus.GoMap.20070223")
> 
> After a LONG time, it stops with the following:
>         Error in as.vector(x, mode) : invalid argument 'mode' error
> 
> Does anyone spot what I'm doing wrong?
> 
> Thanks, Joh
> 
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