[BioC] Problem with invalid GO term in HyperGResult object

[Jenny Drnevich]

Hi Seth,

Once again, updating packages solved the problem!  They must have 
been VERY recent updates - I only installed R-devel last week! I 
guess that's the nature of R, especially right before a new release.

Many thanks,
Jenny

At 11:57 AM 9/11/2007, Seth Falcon wrote:
>Hi Jenny,
>
>Jenny Drnevich <drnevich at uiuc.edu> writes:
> > I posted this message last week, but didn't get any responses. I've
> > been trying everything I can think of to remove this one problematic
> > GO term from my HyperGResult object so I can get the other 45
> > overrepresented GO terms, but I'm not having any luck. I would
> > appreciate any suggestions!!!
>
>Sorry, things have been a bit busy around here :-)
>
> > At 12:22 PM 9/5/2007, Jenny Drnevich wrote:
> >>Hi everyone,
> >>
> >>I'm doing hypergeometric testing of GO terms using GOstats on some
> >>data from ath1121501 Affy arrays. I had some trouble figuring out how
> >>to work with these arrays at first because the annotation package
> >>doesn't include EntrezIDs, but after searching the archives I found
> >>all you had to do was this to get it to work:
> >>
> >>ath1121501ENTREZID <- ath1121501ACCNUM
> >>
> >>Anyway, everything was going fine, expect in one my HyperGResult
> >>objects there is a significant GO term that throws up an error:
> >>
> >>  >SVC.up.BP <- new("GOHyperGParams", geneIds =
> >>entrezUniverse.sortVctrl[EID.sortVctrl==1],
> >>                  universeGeneIds = entrezUniverse.sortVctrl,
> >>annotation = "ath1121501",
> >>                  ontology = "BP", pvalueCutoff = hgCutoff,
> >> conditional = FALSE,
> >>                  testDirection = "over")
> >>
> >>  >SVC.up.BP.results <- hyperGTest(SVC.up.BP)
> >>
> >>  >summary(SVC.up.BP.results)
> >>Error in .checkKeys(value, Lkeys(x), x at ifnotfound) :
> >>    invalid key "GO:0002226"
>
>First, can you try updating your packages.  We've very recently pushed
>out new candidates for annotation as well as some bug fixes for
>AnnotationDbi.
>
>If the problem persists, can you send me (off-list) an rda file
>containing your SVC.up.BP object?
>
>+ seth
>
>--
>Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research Center
>BioC: http://bioconductor.org/
>Blog: http://userprimary.net/user/