[BioC] Gene Ontology relationships

[Seth Falcon]

Hi Dave,

Sorry for the delay in response...

davidl at unr.nevada.edu writes:
> Hello Seth,
>
>      Thank you very much for the response.  I read the help pages for those
> functions and they sound like they are exactly what I was looking for.  I ran
> into a problem actually using termGraphs, however.  This may be something
> simple and stupid but I am having trouble identifying what the problem is. 
> This is the relevant part of my workflow and the resulting error message:
>
>> paramsFvBup<-new("GOHyperGParams", geneIds=llsupFvB,
> universeGeneIds=llsUniversFvB, annotation="mouse4302", ontology="BP",
> pvalueCutoff=0.05, conditional=TRUE, testDirection="over")
>> FvBupOverBP<-hyperGTest(paramsFvBup)
>> htmlReport(FvBupOverBP, file="test.html")
> #That all worked fine and the table looks good
>> termGraphs(FvBupOverBP,pvalue=0.05, use.terms=TRUE)
> Error in "names<-"(`*tmp*`, value = c(NA_character_, NA_character_,
> NA_character_,  :
>         'value' argument must specify unique names

I'm able to reproduce this.  Thanks for the report.  I will look into
it and reply to this thread when I have a fix.  Sorry about that :-P

+ seth

-- 
Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research Center
http://bioconductor.org