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]]

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 l? com os olhos que tem. E interpreta > > A partir de onde os p?s pisam.? > > ? Leonardo Boff ? > > > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- 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

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 – [[alternative HTML version deleted]] [[alternative HTML version deleted]]