[BioC] Annotation parameter of hyperGTest

[James W. MacDonald]

Hi Michael,

Michael Mayhew wrote:
> Greetings,
> 
>    I am using the GOstats package to identify significant association with GO
> terms of a set of "interesting" sequences NOT identified by a microarray.
> 
>    As far as I can tell, I have set up the vectors for the gene universe and
> "interesting" genes correctly. However, I am not sure what to specify for the
> 'annotation' parameter of the GOHyperGParams object.

You will need an annotation package from which you will extract the GO 
information for the test (Seth Falcon may have a way around this, but 
AFAIK there is none). You will need to build one using the AnnBuilder 
package, based on whatever you used to come up with the list of genes 
that you are using.

It might be simpler to use the Category package to do this (but 
regardless, you need to have mappings of genes to GO terms from some source.

Best,

Jim




-- 
James W. MacDonald
University of Michigan
Affymetrix and cDNA Microarray Core
1500 E Medical Center Drive
Ann Arbor MI 48109
734-647-5623



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