[BioC] AnnBuilder GO url question

[Seth Falcon]

Tae-Hoon Chung <thchung at tgen.org> writes:

> Hi, All;
>
> When I tried to build a custom annotation package with AnnBuilder, it
> complained with a warning that it was not able to resolve
> www.godatabase.org¹. 

It seems that either their server is down or the URL has changed.  I
haven't been able to reach their site from a web browser in a few
days.

> (But the process ended smoothly and the package was
> built eventually.) I think this one is due to the global option set in the
> AnnBuilder package for GO url which is
> ³http://www.godatebase.org/dev/database/archive/latest². Question 1. Does
> the fact that R was not able to resolve the Url cause any damage on the
> custom annotation package? 

Well, take a look at what was generated.  But if AnnBuilder can't
access the GO data, then yes this will have bad effect on the GO
annotation!

> Are the GO associations with probes still
> correct? Question 2. What is the correct Url for GO repository in this case?
> How can I reset the global option for GO Url?

I'm not sure what the correct URL is, but we will look into it.  As
for updating/changing the URL that is used, I'm pretty sure there is
documentation on how to do this in the AnnBuilder vignettes.

Best,

+ seth

-- 
Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research Center
http://bioconductor.org