[BioC] error with ontoCompare (goTools)

Mon Jan 19 20:29:11 CET 2009

Hello Wolfgang
I think you have found a bug which I skipped when moving from the old 
annotation system to the current .db based one.
The problem seems to be simply that the internal affy-entrez conversion 
function is not working properly so you must convert it yourself before you 
call "basicProfile"

The following should work while I solve the problem and update the package

require(goProfiles)
require(mouse4302.db)
require(org.Mm.eg.db)
affyPs <- 
c("1415670_at","1415671_at","1415672_at","1415673_at","1415675_at","1415676_a_at","1415677_at","1415678_at","1415679_at")
require(annotate)
entrezs <- getEG (affyPs, "mouse4302.db")
affy.MF <- basicProfile(entrezs, orgPackage = "org.Mm.eg.db", 
anotPackage="mouse4302.db", onto = "MF", level = 2) # "Entrez identifiers 
are the default
printProfiles(affy.MF)

Alex
..............................................................................................................
Alex  Sánchez. Statistics Department. University of Barcelona.
Facultat de Biologia UB. Avda Diagonal 645. 08028 Barcelona. Spain
asanchez_at_ub.edu
Statistics and Bioinformatics Unit
Institut de Recerca. Hospital Universitari Vall 'Hebron
Passeig Vall d'Hebron 112-119. 08034 Barcelona
asanchez_at_ir.vhebron.net
...............................................................................................................

----- Original Message ----- 
From: "Wolfgang Raffelsberger" <wraff at titus.u-strasbg.fr>
To: "Alex Sanchez" <asanchez at ub.edu>
Sent: Monday, January 19, 2009 6:40 PM
Subject: Re: [BioC] error with ontoCompare (goTools)

> Dear Alex,
>
> thank  you for you interesting mail.
> I tried with mouse affy probe-sets but I'm stuck with an error-message, 
> see the following code :
>
> require(goProfiles)
> require(mouse4302.db)
> require(org.Mm.eg.db)
>  # below : some IDs from from Affymetrix mouse4302 array
> affyPs <- 
> c("1415670_at","1415671_at","1415672_at","1415673_at","1415675_at","1415676_a_at","1415677_at","1415678_at","1415679_at")
> affy.MF <- basicProfile(affyPs, idType="BioCprobes", orgPackage = 
> "org.Mm.eg.db", anotPackage="mouse4302.db", onto = "MF", level = 2)
> # here I get :
> Error in eval(expr, envir, enclos) :
>  object "mouse4302.dbENTREZID" not found
> # however, I don't see a package like this on the bioconductor web-site
>
> Have you any ideas/suggestions what I might be doing wrong ?
> Thank's in advance,
> Wolfgang
>
>
> #  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] org.Mm.eg.db_2.2.6  org.Hs.eg.db_2.2.6  mouse4302.db_2.2.5 
> goProfiles_1.4.0    GO.db_2.2.5         RSQLite_0.7-1     [7] DBI_0.2-4 
> AnnotationDbi_1.4.2 Biobase_2.2.1       svSocket_0.9-5      svIO_0.9-5 
> R2HTML_1.59       [13] svMisc_0.9-5        svIDE_0.9-5
>
> Alex Sanchez a écrit :
>> 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
>>>
>>>
>>
>> _______________________________________________
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>>
>>
>
>
> -- 
> . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
> 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
> http://www-bio3d-igbmc.u-strasbg.fr/~wraff
> wolfgang.raffelsberger at igbmc.fr
>
>
>