[BioC] problem with makeGOGraph function

Samuel Rochette [guest] guest at bioconductor.org
Thu Mar 27 19:51:26 CET 2014


I wish to produce a directed acyclic graph of a gene enrichment analysis that I performed using R GOstats package. For this, I wanted to use the makeGOGraph function, but it seems that there is a problem when using the yeast data base package "org.Sc.sgd.db".

Here is the command line:

> tree <- makeGOGraph(hits.list[[1]]$sys, Ontology="BP", removeRoot=TRUE,chip="org.Sc.sgd.db")

where "hits.list[[1]]$sys" is a vector containing yeast genes. 

 -- output of sessionInfo(): 

Here is the error message:

"Erreur dans .get_eg_to_go_fun(mapfun, chip) : 
  either mapfun or chip must be specified
De plus : Message d'avis :
objet 'org.Sc.sgdGO2PROBE' introuvable 
DB-based version of  org.Sc.sgd.db  not found. 
Reverting to use of environment-based GO"

It seems that there is something missing in the org.Sc.sgd.db package but I could not find out what exactly.

Thank you for your help!

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