[BioC] error with ontoCompare (goTools)

[Martin Morgan]

Hi Wolfgang --

Wolfgang Raffelsberger <wraff at titus.u-strasbg.fr> writes:

> 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 ...

I think this is an issue with the interaction between annotate and
goTools. Both define a function getOntology. I guess your search()
path has annotate in front of goTools. goTools does not have a name
space. When it looks for getOntology, it finds the version that is
'first' on the search path. This is the annotate version.

Two short term solutions are to arrange your search path so that
goTools is before annotate (e.g., by library(annotate) before
library(goTools)) or temporarily masking the annotate version of the
function

> getOntology <- goTools::getOntology
> res0 <- ontoCompare(affylist2, probeType = "hgu133a", plot=T)
> rm(getOntology)

A longer term solution is for the maintainer of goTools (cc'd) to add
a name space (perhaps using the experimental package codetoolsBioC
available in the bioc devel repository to help identify appropriate
imports) so that code in the goTools package is guaranteed to find the
right version of the function.

Martin


> 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
>
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-- 
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109

Location: Arnold Building M2 B169
Phone: (206) 667-2793