[BioC] OntoCompare Error

[Paquet, Agnes]

Hi Johannes,
 
Did you feed a list of GO ids or a vector? of GO ids? I took some of your ids to try to reproduce the error but I didn't get any. Here is what I did:
 
mygo=c("GO:0003677", "GO:0004386", "GO:0005524", "GO:0016787", "GO:0001882",
  "GO:0003779", "GO:0005509", "GO:0005515", "GO:0042803", "GO:0051015",
  "GO:0003677", "GO:0003700", "GO:0005515", "GO:0008270", "GO:0043565",
  "GO:0046872", "GO:0000166", "GO:0003774", "GO:0003779", "GO:0005515")

ontoCompare(list(mygo),plot=T,probeType="GO")
 
My R information is:
> sessionInfo()
R version 2.4.0 (2006-10-03) 
i386-pc-mingw32 
locale:
LC_COLLATE=English_United States.1252;LC_CTYPE=English_United States.1252;LC_MONETARY=English_United States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252
attached base packages:
[1] "tools"     "methods"   "stats"     "graphics"  "grDevices" "utils"    
[7] "datasets"  "base"     
other attached packages:
 goTools       GO annotate  Biobase 
 "1.6.0" "1.14.1" "1.12.0" "1.12.2" 

 
If you are feeding a vector of length 14000, ontoCompare is going to see your argument as a list of 14000 unique entities and that may be a reason for the error.
If you are using the same type of input, could you please send me some of your GO ids in a .txt file, the command you are using and some information about which version of R, GO and goTools you are using so that I can reproduce the error and try to fix the problem? 
 
Best,
 
Agnes
 

________________________________

From: bioconductor-bounces at stat.math.ethz.ch on behalf of Johannes Graumann
Sent: Mon 2/26/2007 4:16 AM
To: bioconductor at stat.math.ethz.ch
Subject: Re: [BioC] OntoCompare Error



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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