[BioC] topGO in combination with Agilent arrays

[James W. MacDonald]

Hi Patrick,

On 9/12/2010 3:04 PM, De Boever Patrick wrote:
> Dear all,
>
> I’m working with Agilent 4X44K microarrays (annotation db
> hgug4112a.db) and a genelist with differentially expressed genes with
> Agilent Ids. I would like to try topGO for GO analysis. I have read
> the vignette but find it difficult to translate the code to fit my
> purpose. How should the code mentioned below be adapted:
>> sampleGOdata<- new("topGOdata", description = "Simple session",
>> ontology = "BP",allGenes = geneList, geneSel = topDiffGenes,
>> nodeSize = 10, annot = annFUN.db, affyLib = affyLib)
>
> Any example on topGO using other examples would be helpful.

I see you are working through the topGO vignette. As part of that 
effort, it might be worth it to look at the objects are being used as 
part of the vignette, so you might be able to create something similar 
using your data.

For instance:

 > head(geneList)
1095_s_at   1130_at   1196_at 1329_s_at 1340_s_at 1342_g_at
1.0000000 1.0000000 0.6223795 0.5412240 1.0000000 1.0000000

Which in the text is described as the probeset IDs and p-values for 323 
of the probesets on the hgu95av2 chip. Now I suppose you have some data 
and corresponding p-values, so I leave it up to you to create a similar 
named vector, using your data.

The only other thing that will be different is the argument for affyLib.

Just two code chunks prior to the one you note in your email, you can 
see where the affyLib comes from. It might be a bit obscure what that is 
exactly, but you _could_ install the ALL package yourself, submit that 
code, and see for your self what the affyLib object is.

But to save you that effort, as the ALL package is a bit large, it is 
simply the name of the annotation package. So you could just use affyLib 
= "hgug4112a.db".

Best,

Jim


>
> Thank you for your support,
>
> Patrick De Boever
>
>
> Patrick De Boever, PhD, MSc Flemish Institute for Technological
> Research (VITO) Unit Environmental Risk and Health, Toxicology group
> Industriezone Vlasmeer 7, 2400 Mol, Belgium Tel.   + 32 14 33 51 45
> Fax.  + 32 14 58 05 23
> patrick.deboever at vito.be<mailto:patrick.deboever at vito.be>
>
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-- 
James W. MacDonald, M.S.
Biostatistician
Douglas Lab
University of Michigan
Department of Human Genetics
5912 Buhl
1241 E. Catherine St.
Ann Arbor MI 48109-5618
734-615-7826
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