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.org?
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
> ?http://www.godatebase.org/dev/database/archive/latest?. 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
Hi, Tae-Hoon,
Even if accessing GO website is a problem, it won't affect your custom
annotation package. There are only 3 objects in the custom package
that are
related to GO: <pkg>GO, <pkg>GO2PROBE and <pkg>GO2ALLPROBES. Here I
use <pkg> to
represent your package name. <pkg>GO and <pkg>GO2PROBE are created by
using
direct mapping relations between gene and GO obtained from Entrez Gene
website.
<pkg>GO2ALLPROBES is created by using <pkg>GO2PROBE and the GO package
in
bioconductor. So, you don't need access to GO website. But this is
just based on
my own understanding of AnnBuilder. You can check the quality control
data of
your package to make sure the GO annotation is OK. In R, load your
package and
type "<pkg>()" (replace <pkg> with your package name). If the numbers
are
reasonable, then everything is fine.
Which GO package in bioconductor are you using now? We are updating
the GO
package in bioc 2.0 now. If you are using GO 1.15.12, you may want to
wait a
week until a more stable GO is available.
hope this is helpful
nianhua
