Greetings R users,
I have a rather specific question I hope someone could assist me with.
I have been using the topGO package for some Gene Ontology analysis of some
RNA-seq data. As such I use a organism database from the biomaRt library.
I can create a topGOdata object with the following command
GOdata=new("topGOdata", ontology="BP", allGenes=geneList,
nodeSize=10,
annot=annFUN.org,
mapping="org.Ss.eg.db",
ID="Symbol")
Everything works well except when I wish to look at the genes within an
individual GO where I can't get the function to work.
I initially thought to try this because I don't use a microarray library:
gt=printGenes(GOdata, whichTerms = goID, chip="org.Ss.eg.db", numChar = 40)
but I received the error:
Error in get(paste(chip, "ENTREZID", sep = "")):
object 'org.Ss.egENTREZID' not found
Has anyone experienced this or have any thoughts?
Regards,
--
Charles Determan
Integrated Biosciences PhD Student
University of Minnesota
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