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

[Jenny Drnevich]

>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
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e-mail: drnevich at uiuc.edu