Hi Marc,

Yes, the organism would be homo sapiens.




----- Original Message ----
From: Marc Carlson <mcarlson@fhcrc.org>
To: Paul Evans <p.evans48@yahoo.com>
Cc: Bioconductor@stat.math.ethz.ch
Sent: Wednesday, March 26, 2008 12:05:20 PM
Subject: Re: [BioC] Newbie question on GOstats (hyperGTest) for dual channel (from SMD) arrays

Paul Evans wrote:
> Hi,
>
> I had a microarray dataset (dual channel taken from Stanford Microarray Database) of 20,000 genes. I have used a filtering technique to reduce this to about 2500 genes. I now want to perform clustering and use the hyperGTest, as given in the GOstats:
>
>  hgCutoff <- 0.001
>  params <- new("GOHyperGParams", geneIds = selectedEntrezIds,
>  universeGeneIds = entrezUniverse, annotation = "hgu95av2",
>  ontology = "BP", pvalueCutoff = hgCutoff, conditional = FALSE,
>  testDirection = "over")
>
>
> I understand that the universeGeneIds will be the entrez ids of the 2500 genes, and that the selectedEntrezIds are the entrez ids of the genes in a cluster, but what should I choose as the annotation package? I don't think the SMD gives the details of the array that was used. 
>
> many thanks!
>
>
>
>
>
>
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>  
Do you know what organism are the data from?

Marc


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