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

[michael watson (IAH-C)]

Hi

Thanks for all of the replies!

I am getting there slowly - please someone point to an obvious tutorial
if I have missed it!  I've read the annotate vignette...

I have the metaData package for hu6800, GO, and KEGG.  And I can do
stuff like this:

l <- get("X65663_at",env=hu6800GO)
names(l)
get("GO:0006325", env=GOTERM)

What I want to do is look at groups of genes that I have found and see
if they make sense.  By make sense, I mean "do they have similar or
related functions", "do they appear in the same pathway" etc etc.  

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?

Cheers
Mick

-----Original Message-----
From: Sean Davis [mailto:sdavis2 at mail.nih.gov] 
Sent: 04 February 2005 14:31
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 4, 2005, at 9:05 AM, michael watson ((IAH-C)) wrote:

> Hi
>
> The golub dataset has identifiers which I can only assume are based on

> GenBank/EMBL accession numbers (Eg M71243_f_at, U29175_at etc).
>

These are affy id's, I think from the Hgu95a array?  In any case, you 
can use the annotate,GOstats, etc. packages with the appropriate 
annotation package (Like I said, I think 95a array).  Check out the 
vignette on using the annotate package as a start.

> I want to enrich the annotation for this data set by mapping these 
> identifiers to GO terms, KEGG pathways etc but I can't figure out how 
> to do it using bioconductor.
>
> Can anyone give me a few tips?
>
> Mick
>
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