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

[Jenny Drnevich]

Well, it's good to know that I'm not a _complete_ idiot :)  I didn't 
realize GO was an annotation/metadata package and not a software 
package, which is why I couldn't find it on the website. I was able 
to build from source for the newest versions of GO and GO.db, and the 
problem with invalid GO terms went away... but then I also built the 
newest version of the ath1121501 annotation package, and then calling 
hyperGTest() lead to the following error:

Error in getUniverseHelper(probes, datPkg, entrezIds) :
   No Entrez Gene ids left in universe


ARRRGHH! Anyway, I think I'll wait until Tuesday (I'm off on 
Monday!!) when the windows binaries are hopefully available, update 
all my packages again, and then see what happens...

Thanks for all your help,
Jenny

At 01:36 PM 9/14/2007, Robert Gentleman wrote:
>Hi Jenny,
>   It seems that the piece that produces windows binaries of the 
> annotation packages has been broken.  We should be able to push new 
> versions first thing on Monday.  If you have the ability to build 
> windows packages, you could do that directly from the source package.
>
>   sorry about that
>    Robert
>
>
>Jenny Drnevich wrote:
>>>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
>>As of 2 minutes ago, these were the only packages that it updated...
>>package 'affyio' successfully unpacked and MD5 sums checked
>>package 'annaffy' successfully unpacked and MD5 sums checked
>>package 'annotate' successfully unpacked and MD5 sums checked
>>package 'AnnotationDbi' successfully unpacked and MD5 sums checked
>>package 'biomaRt' successfully unpacked and MD5 sums checked
>>package 'Category' successfully unpacked and MD5 sums checked
>>package 'GOstats' successfully unpacked and MD5 sums checked
>>package 'graph' successfully unpacked and MD5 sums checked
>>package 'preprocessCore' successfully unpacked and MD5 sums checked
>>... and I'm still having the same problem. I also tried using 
>>biocLite("GO"), but it downloaded the same version I already had: 
>>1.17.0.  If there's a newer version, it's not available as a 
>>Windows binary. BTW, there is no package "GO" on the BioC website 
>>software listings for either BioC 2.0 or BioC 2.1...
>>Thanks,
>>Jenny
>>
>>
>>>--
>>>Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research Center
>>>BioC: http://bioconductor.org/
>>>Blog: http://userprimary.net/user/
>>Jenny Drnevich, Ph.D.
>>Functional Genomics Bioinformatics Specialist
>>W.M. Keck Center for Comparative and Functional Genomics
>>Roy J. Carver Biotechnology Center
>>University of Illinois, Urbana-Champaign
>>330 ERML
>>1201 W. Gregory Dr.
>>Urbana, IL 61801
>>USA
>>ph: 217-244-7355
>>fax: 217-265-5066
>>e-mail: drnevich at uiuc.edu
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>
>--
>Robert Gentleman, PhD
>Program in Computational Biology
>Division of Public Health Sciences
>Fred Hutchinson Cancer Research Center
>1100 Fairview Ave. N, M2-B876
>PO Box 19024
>Seattle, Washington 98109-1024
>206-667-7700
>rgentlem at fhcrc.org

Jenny Drnevich, Ph.D.

Functional Genomics Bioinformatics Specialist
W.M. Keck Center for Comparative and Functional Genomics
Roy J. Carver Biotechnology Center
University of Illinois, Urbana-Champaign

330 ERML
1201 W. Gregory Dr.
Urbana, IL 61801
USA

ph: 217-244-7355
fax: 217-265-5066
e-mail: drnevich at uiuc.edu