[BioC] help with makeGOGraph

Fri Nov 12 19:09:40 CET 2010

Hello again,

I have completely forgotten to copy my session informations...

> sessionInfo()

R version 2.12.0 (2010-10-15)

Platform: i386-pc-mingw32/i386 (32-bit)

locale:

[1] LC_COLLATE=French_France.1252  LC_CTYPE=French_France.1252   

LC_MONETARY=French_France.1252

[4] LC_NUMERIC=C                   LC_TIME=French_France.1252    

attached base packages:

[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:

 [1] ecoli2cdf_2.6.0       gage_2.0.0            multtest_2.6.0       

ecoli2.db_2.4.7       org.EcK12.eg.db_2.4.6

 [6] simpleaffy_2.26.0     gcrma_2.22.0          genefilter_1.32.0    

annotate_1.28.0       biomaRt_2.6.0        

[11] annaffy_1.22.0        KEGG.db_2.4.5         GO.db_2.4.5          

lattice_0.19-13       affy_1.28.0          

[16] limma_3.6.0           GOstats_2.16.0        RSQLite_0.9-2        

DBI_0.2-5             graph_1.28.0         

[21] Category_2.16.0       AnnotationDbi_1.12.0  Biobase_2.10.0       

loaded via a namespace (and not attached):

 [1] affyio_1.18.0         Biostrings_2.18.0     grid_2.12.0          

GSEABase_1.12.0       IRanges_1.8.0        

 [6] MASS_7.3-8            preprocessCore_1.12.0 RBGL_1.25.1          

RCurl_1.4-4.1         splines_2.12.0       

[11] survival_2.35-8       tools_2.12.0          XML_3.2-0.1          

xtable_1.5-6         

As for an example if I use the following vector of EntrezGeneIds I get a

similar error message:

>ex=c(947043,948258,2847747,2847746,946713,948679,948192,944872,946844,946841)

> ex

 [1]  947043  948258 2847747 2847746  946713  948679  948192  944872 

946844  946841

>    makeGOGraph(ex,ontology="BP",removeRoot=T,mapfun=NULL,chip=ecoli2.db)

Erreur dans makeGOGraph(ex, ontology = "BP", removeRoot = T, mapfun =

NULL,  : 

  argument(s) inutilisé(s) (ontology = "BP")

Clémentine

On Fri, 12 Nov 2010 09:12:18 -0800, Marc Carlson <mcarlson at fhcrc.org>

wrote:

> Hi Clémentine,

> 

> Could you please give us your sessionInfo() and a reproducible example? 

> That would allow us to be able to really find out what is happening

> here.  You might want find it helpful to have a peek at the posting

> guide here:

> 

> http://www.bioconductor.org/help/mailing-list/posting-guide/

> 

> 

>   Marc

> 

> 

> 

>  

> On 11/12/2010 07:51 AM, Clémentine Dressaire wrote:

>> Dear BioC users,

>>

>>

>>

>> I am trying to construct a GOgraph using a gene list (overgenes[,3]) of

>>

>> messengers that I previously identified as overexpressed in the

>> condition I

>>

>> was interested in. I previoulsy used this same gene list to perform

>>

>> hypergeometric tests and it worked well. 

>>

>>

>>

>> With makeGOgraph I systematically get the following error message,

>>

>> whichever ontology type I try to use:

>>

>>     

>>

>>

makeGOGraph(overgenes[,3],ontology="BP",removeRoot=F,mapfun=NULL,chip=ecoli2.db)

>>

>>                                  

>>

>>      Erreur dans makeGOGraph(overgenes[, 3], ontology = "BP",

removeRoot

>>      =

>>

>> F,  : 

>>

>>      argument(s) inutilisé(s) (ontology = "BP")

>>

>>

>>

>> I wonder wether this could be due to the fact that some of the genes in

>>

>> the list do not have GO annotation...(then does it mean that I have to

>>

>> eliminate them? If so what would be the simplest way?)

>>

>>

>>

>> Does anyone can throw light on this issue for me?

>>

>>

>>

>> Many thanks for your help,

>>

>>

>>

>> Clémentine

>>

>>

>>

>>

>>

>>

> 

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-- 

Clémentine Dressaire

Post-doctoral research fellow

Control of gene expression lab

ITQB - Instituto de Tecnologia Química e Biológica

Apartado 127, Av. da República

2780-157 Oeiras

Portugal

+351 214469562