[BioC] Getting GO terms and other annotation for Golub data set

[michael watson (IAH-C)]

Thanks Sean.

I don't know whether my installation of GOstats has gone awry at some
point, but there doesn't seem to be a manual or vignette for the package
in C:\Program Files\R\rw2001\library\GOstats\doc.  There is an
index.html but it is next to empty.

So if I have two affy ids, I can get the GO terms easily, but it's not
immediately obvious which functions in GOstats I could use to to see if
those two affy ids are related in a functional sense.

-----Original Message-----
From: Sean Davis [mailto:sdavis2 at mail.nih.gov] 
Sent: 07 February 2005 13:05
To: michael watson (IAH-C)
Cc: bioconductor at stat.math.ethz.ch
Subject: Re: [BioC] Getting GO terms and other annotation for Golub data
set



On Feb 7, 2005, at 5:21 AM, michael watson ((IAH-C)) wrote:
>
> So now I have the GO and KEGG metaData packages, and I know how to
> query
> them at a very low level.  My next step will be to write some code to
> take a group of affy identifiers, query these packages and see if they
> all seem to hit the same KEGG pathway, or have GO terms in common.
Has
> anyone done this before and put it in a nice package, or do I write it
> from scratch?
>

The GOstats package does this for GO.  You could use that directly for 
the GO stuff.  For the KEGG stuff, I think you would have to write 
something, but it shouldn't be too hard.  Also, there are now several 
websites that allow you to do this (not an R solution, but perhaps a 
good first-pass).

Sean