[BioC] error with ontoCompare (goTools)

[Alex Sanchez]

Hi WolfgangYou may want to try the 'goProfiles' package which is intended to 
do exactly what you're asking for, that is comparing two gene lists at a 
given level of the GO.I'd be happy to help if there appear any problems or 
to (try to) adapt any improvements you may 
suggest.BestAlex---------------------------------------------------Alex 
SánchezStatistics Department. University of Barcelona. Facultat de Biologia 
UB. Avda Diagonal 645. 08028 Barcelona. Spainmail 
asanchez_at_ub.eduStatistics and Bioinformatics UnitInstitut de Recerca. 
Hospital Universitari Vall 'HebronPasseig Vall d'Hebron 112-119. 08034 
Barcelonamail 
asanchez_at_ir.vhebron.net---------------------------------------------------->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
>
>