[BioC] topGO w/custom annotation

[James W. MacDonald]

Hi Sebasien,

Sebastien Gerega wrote:
> Hi,
> I would like to identify overrepresented GO in my dataset using the 
> topGO package.
> I am working with a C. neoformans oligo array and have the GO annotation 
> in a list with the following format:
> 
> $`162.m02116`
> [1] GO:0009536
> 4026 Levels: GO:0 GO:00 GO:000 GO:0000 GO:00000 GO:000000 GO:0000001 
> GO:0000002 GO:0000004 GO:0000006 GO:0000009 GO:0000010 ... GO:0051861
> 
> $`162.m02150`
> [1] GO:0009536
> 4026 Levels: GO:0 GO:00 GO:000 GO:0000 GO:00000 GO:000000 GO:0000001 
> GO:0000002 GO:0000004 GO:0000006 GO:0000009 GO:0000010 ... GO:0051861
> 
> $`162.m02156`
> [1] GO:0005554 GO:0008372 GO:0000004
> 4026 Levels: GO:0 GO:00 GO:000 GO:0000 GO:00000 GO:000000 GO:0000001 
> GO:0000002 GO:0000004 GO:0000006 GO:0000009 GO:0000010 ... GO:0051861
> 
> How do I go about creating the GOdata object?
> 
> GOdata = new("topGOdata",
>            ontology = "MF",
>            allGenes = selectedList,
>            annot = annFUN.GO2genes,  ## the new annotation function
>            GO2genes = myGO2genes)    ## the GO to gene ID's dataset
> 
> Specifically what do I use for the annotation function? It is unclear to 
> me how to write this aspect.

The documentation is a bit unclear, but I believe you have things set up 
correctly. I assume you have done the rest of the analysis and had no 
errors?

Best,

Jim


> Am I correct in understanding that I supply my list as the final argument?
> thanks,
> Sebastien
> 
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-- 
James W. MacDonald, M.S.
Biostatistician
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623