Question: problem with makeGOGraph function
5.7 years ago by
Guest User • 12k
Guest User • 12k wrote:
Hi, 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[]$sys, Ontology="BP", removeRoot=TRUE,chip="org.Sc.sgd.db") where "hits.list[]$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! -- Sent via the guest posting facility at bioconductor.org.
ADD COMMENT • link •