Hi Renata,
 can you provide you sessionInfo()
and a reproducible example?

thanks

Anna

 Anna Freni Sterrantino
Ph.D Student 
Department of Statistics
University of Bologna, Italy
via Belle Arti 41, 40124 BO.




________________________________
Da: Renata Paiva <rtpaivabr@yahoo.com.br>
A: bioconductor@stat.math.ethz.ch
Inviato: Martedì 26 maggio 2009, 19:06:08
Oggetto: [BioC] function error

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 – 




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