[BioC] GOstats different goDag size just changing the

[James W. MacDonald]

Hi Cristobal,

On 10/16/2012 4:44 PM, Cristobal Fresno Rodríguez wrote:
> Dear list,
>
> I am trying to use GOstats using "under" and "over" testDirection. But,
> the hyperGTest builds two diferent goDags. Shouldn't they be of the same
> size??

No. The testDirection refers to over-represented and under-represented 
GO terms, so they should be mutually exclusive given the same data set.

Best,

Jim


>
> Thanks,
>
> Cristobal
>
>> library(GOstats)
>> load(file="Genes.RData"); genesModel<- out; rm(out)
>> univer<- unique(as.character(genesModel$GeneID))
>> paramsOver<- new("GOHyperGParams",
> +   geneIds= univer[1:100],
> +   universeGeneIds=univer[1:200],
> +   annotation="org.Mm.eg.db",
> +   ontology="BP",
> +   pvalueCutoff=0.01,
> +   conditional=FALSE,
> +   testDirection="over")
> Loading required package: org.Mm.eg.db
>
>> paramsUnder<- new("GOHyperGParams",
> +   geneIds= univer[1:100],
> +   universeGeneIds=univer[1:200],
> +   annotation="org.Mm.eg.db",
> +   ontology="BP",
> +   pvalueCutoff=0.01,
> +   conditional=FALSE,
> +   testDirection="under")
>
>> over<- hyperGTest(paramsOver)
>> under<- hyperGTest(paramsUnder)
>> over
> Gene to GO BP  test for over-representation
> 1146 GO BP ids tested (0 have p<  0.01)
> Selected gene set size: 80
>      Gene universe size: 156
>      Annotation package: org.Mm.eg
>> under
> Gene to GO BP  test for under-representation
> 1776 GO BP ids tested (0 have p<  0.01)
> Selected gene set size: 80
>      Gene universe size: 156
>      Annotation package: org.Mm.eg
>> length(pvalues(over))
> [1] 1146
>> length(pvalues(under))
> [1] 1776
>
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-- 
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099