[BioC] error with ontoCompare (goTools)

[Wolfgang Raffelsberger]

Just as additional information :
I found out that this problem might to be specific to Windows (with 
R-2.8.0). I managed to run the same code on Linux with R-2.8.0 without 
the error message ...

Wolfgang

 > sessionInfo()
R version 2.8.0 (2008-10-20)
x86_64-unknown-linux-gnu

locale:
C

attached base packages:
[1] tools     stats     graphics  grDevices utils     datasets  methods 
[8] base    

other attached packages:
[1] hgu133a.db_2.2.5    goTools_1.16.0      GO.db_2.2.5       
[4] RSQLite_0.7-1       DBI_0.2-4           AnnotationDbi_1.4.1
[7] Biobase_2.2.1 



Wolfgang Raffelsberger a écrit :
> Dear list,
> I'm interested in making a graph (pie-chart or similar) showing the 
> different GO ontologies one may get from a list of genes (in my case a 
> list of Affymetrix probe-sets).  In this context it might be good only 
> to compare a given level of GO-ontologies (to avoid redundancies with 
> terms closer to the root), ideally I'd like use something close to 
> GO-slim.
>
> It looks like that goTools allows to do something close to what I'm 
> interested (without the GOslim...).
> So I tried to use goTools but running the code from the documentation 
> (as suggested in ?ontoCompare ) I got the following error :
>
> library(goTools)
> library(GO.db)
> data(probeID)
> affylist2 <- list(L4 <- affylist[[1]][1:5], L5 <- 
> affylist[[2]][1:4])   # shorter list just for testing ...
> res0 <- ontoCompare(affylist2, probeType = "hgu133a", plot=T)
>
> and I get the following (error) message :
>
> Starting ontoCompare...
> Error in FUN(X[[1L]], ...) :
>  unused argument(s) (list(`GO:0000001` = <S4 object of class 
> "GOTerms">, `GO:0000002` = <S4 object of class "GOTerms">, 
> `GO:0000003` = <S4 object of class "GOTerms">, `GO:0000006` = <S4 
> object of class "GOTerms">, `GO:0000007` = <S4 object of class 
> "GOTerms">, `GO:0000009` = <S4 object of class ...
>
> Am I missing somthing ?
> Other suggestions ?
>
> Thank's for any hints,
> Wolfgang
>
>
> Just for completeness:
> sessionInfo()
>
> R version 2.8.1 (2008-12-22)
> i386-pc-mingw32
>
> locale:
> LC_COLLATE=French_France.1252;LC_CTYPE=French_France.1252;LC_MONETARY=French_France.1252;LC_NUMERIC=C;LC_TIME=French_France.1252 
>
>
> attached base packages:
> [1] tools     stats     graphics  grDevices datasets  tcltk     
> utils     methods   base   
> other attached packages:
> [1] hgu133a.db_2.2.5    annotate_1.20.1     xtable_1.5-4        
> goTools_1.16.0      GO.db_2.2.5       [6] RSQLite_0.7-1       
> DBI_0.2-4           AnnotationDbi_1.4.2 Biobase_2.2.1       
> svSocket_0.9-5    [11] svIO_0.9-5          R2HTML_1.59         
> svMisc_0.9-5        svIDE_0.9-5  
>
>

. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Wolfgang Raffelsberger, PhD
Laboratoire de BioInformatique et Génomique Intégratives
CNRS UMR7104, IGBMC 
1 rue Laurent Fries,  67404 Illkirch  Strasbourg,  France
Tel (+33) 388 65 3300         Fax (+33) 388 65 3276
wolfgang.raffelsberger (at) igbmc.fr