[BioC] function error

[Martin Morgan]

Hi Renata --

what does

> sessionInfo()

say? Are you using the current version of R (2.9), and have you
followed the direction to "Update installed Bioconductor packages", at

  http://bioconductor.org/docs/install/

? It is best to paste the exact R commands used into the email
message, in the exact order they were used.

Hope that helps.

Martin

"Renata Paiva" <rtpaivabr at yahoo.com.br> writes:

>  I tried to use the function HyperGTest()  with GO, and it gives the error:
>
>  
>
> Erro em initialize(value, ...) : 
>
>   invalid names for slots of class "GOHyperGResult": pvalues, oddsRatios,
> expectedCounts, catToGeneId
>
>  
>
> I’m using this packages
>
>  
>
> library(org.Hs.eg.db)
>
> library(annotate)
>
> library(GO.db)
>
> library(RColorBrewer)
>
> library(xtable)
>
> library(Rgraphviz)
>
> library(Category)
>
> library(GOstats)
>
>  
>
> I defined the class: 
>
> params = new("GOHyperGParams", geneIds = (corte), universeGeneIds = (univ),
>
>                 annotation = "org.Hs.eg.db", ontology = "BP",   pvalueCutoff
> = hgCutoff, 
>
> conditional = TRUE, testDirection = "over")
>
>  
>
> where: 
>
> corte = genes selected with an ftest (GO)
>
> univ = gene universe (GO)
>
>  
>
> And the function is 
>
>  I tried to use the function HyperGTest()  with GO, and it gives the error:
>
>  
>
> Erro em initialize(value, ...) : 
>
>   invalid names for slots of class "GOHyperGResult": pvalues, oddsRatios,
> expectedCounts, catToGeneId
>
>  
>
> I’m using this packages
>
>  
>
> library(org.Hs.eg.db)
>
> library(annotate)
>
> library(GO.db)
>
> library(RColorBrewer)
>
> library(xtable)
>
> library(Rgraphviz)
>
> library(Category)
>
> library(GOstats)
>
>  
>
> I defined the class: 
>
> params = new("GOHyperGParams", geneIds = (corte), universeGeneIds = (univ),
>
>                 annotation = "org.Hs.eg.db", ontology = "BP",   pvalueCutoff
> = hgCutoff, 
>
> conditional = TRUE, testDirection = "over")
>
>  
>
> where: 
>
> corte = genes selected with an ftest (GO)
>
> univ = gene universe (GO)
>
>  
>
> hgOver = hyperGTest(params)
>
>  
>
> thanks
>
>  
>
> Renata Paiva
>
>  
>
>  
>
> “Ler significa reler e compreender, interpretar. 
>
> Cada um lê com os olhos que tem. E interpreta
>
> A partir de onde os pés pisam.” 
>
> – Leonardo Boff – 
>
>  
>
>
> 	[[alternative HTML version deleted]]
>
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-- 
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109

Location: Arnold Building M1 B861
Phone: (206) 667-2793