[BioC] Problem with invalid GO term in HyperGResult object - NOT solved

[Seth Falcon]

Jenny Drnevich <drnevich at uiuc.edu> writes:

> Hi Seth,
>
> I had a problem earlier with an invalid GO term that was throwing up
> an error. You advised to update all my packages, which I thought
> solved the problem. However, the problem reappeared later when I reran
> my script, and I've figured out the difference is what other packages
> I have loaded. I have a complete R session below, where I first only
> load GOstats, then call hyperGTest on a GOHyperGParams object, which
> tests 1139 GO BP ids, and 44 have p < 0.001. Next I load
> affycoretools, then call hyperGTest on the exact same object, which
> now tests 1146 GO BP ids, and 46 have p < 0.001. Loading affycoretools
> in turn loads package GO, which then masks many functions from package
> GO.db - maybe this is where the problem is?  I'm fine because I can
> get the problematic GO term to disappear, but it seems like the
> discordance between the packages is a bug.

Yes, this is not as desired.  But can you please try updating the GO
package and see if this remains to be an issue :-)

BTW, I believe this hasn't changed since your last update so I will
recommend how to update:

library(Biobase)
update.packages(repos=biocReposList())

+ seth

-- 
Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research Center
BioC: http://bioconductor.org/
Blog: http://userprimary.net/user/