[BioC] Gene Ontology relationships

[davidl at unr.nevada.edu]

Hello Seth,

     That was really fast.  I'm going to try out this new version as soon as I
get back to the computer with the data and let you know how it goes.  You are
awesome.

Thanks sir,

Dave


Quoting Seth Falcon <sfalcon at fhcrc.org>:

> Hi,
>
> > 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 believe that I've fixed the problem.  GOstats_2.2.5 is available via
> biocLite (not yet for OS X).  In the meantime, I noticed a labeling
> problem with plotGOTermGraph and GOstats_2.2.6 will be available in
> the next couple of days.
>
> Please let me know if you encounter further problems --- these
> functions for extracting subgraphs of the results and plotting are
> quite new and somewhat experimental so I'm open to suggestions.
>
> Best,
>
> + seth
>
> --
> Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research Center
> http://bioconductor.org
>