Error with the function hyperGtest from GOstats package

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ADD COMMENT • link updated 18.1 years ago by James W. MacDonald 68k • written 18.1 years ago by Anne.Biton@sanofi-aventis.com ▴ 20

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James W. MacDonald 68k

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Hi Anne, Anne.Biton at sanofi-aventis.com wrote: > Dear all, > > I have one subset of GO Ids and one set of Gene EntrezIds. > I'm trying to perfom an hyperGTest and I want to restrict the annotation > to my subset of GO ids. > > So, I define a GOHyperGParams object (I use the slot "catogrySubsetIds" > to restrict to my GO Ids) > >>params = new ("GOHyperGParams",geneIds = genes, universeGeneIds = > > univers, annotation = "hgu133a", cateogrySubsetIds = GOBPselec) > > where GOBPselec is a vector of GO Ids : > >>GOBPselec > > [1] "GO:0006915" "GO:0007165" "GO:0006468" "GO:0006350" "GO:0006508" > "GO:0008152" "GO:0000004" "GO:0006355" "GO:0006457" "GO:0007242" > "GO:0006512" ...... > > And finally, I launch the test and I have the following error : > >>hg = hyperGTest(params) > > "Error in getGoToProbeMap(go2allprobes, ontology) : > incorrect type of index" > > I know that this error come from "cateogrySubsetIds" but I don't > understand why? I don't think it comes from cateogrySubsetIds, but from the fact that you aren't passing anything in for the 'ontology' slot. Try adding an ontology = "BP" to your call to new("GOHyperGParams", ...). Best, Jim > The description of this slot is : <<object of="" class="" "any":="" if="" the="" test=""> method supports it, can be used to specify a subset of category ids to > include in the test instead of all possible category ids. >> > > Best regards, > Anne. > > > > > > > > [[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 -- James W. MacDonald, M.S. Biostatistician Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues.

ADD COMMENT • link 18.1 years ago James W. MacDonald 68k

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Thanks James, (sorry for the stupid error!) In fact, now I return to my first problem : the slot catogrySubsetIds isn't taken into account : the annotation seems to be done on all GO Ids in the two cases : > params = new ("GOHyperGParams",geneIds = genes, universeGeneIds = univers, annotation = "hgu133a", ontology = "BP") > hgtest = hyperGTest(params) > params = new ("GOHyperGParams",geneIds = genes, universeGeneIds = univers, annotation = "hgu133a", ontology = "BP",cateogrySubsetIds = GOBPselec) > hgtest2 = hyperGTest(params) > hgtest2 Gene to GO BP test for over-representation 566 GO BP ids tested (11 have p < 0.01) Selected gene set size: 155 Gene universe size: 7620 Annotation package: hgu133a > hgtest Gene to GO BP test for over-representation 566 GO BP ids tested (11 have p < 0.01) Selected gene set size: 155 Gene universe size: 7620 Annotation package: hgu133a Best, Anne. -----Message d'origine----- De : James W. MacDonald [mailto:jmacdon at med.umich.edu] Envoy? : jeudi 15 mars 2007 14:19 ? : Biton, Anne PH/FR Cc : bioconductor at stat.math.ethz.ch Objet : Re: [BioC] Error with the function hyperGtest from GOstats package Hi Anne, Anne.Biton at sanofi-aventis.com wrote: > Dear all, > > I have one subset of GO Ids and one set of Gene EntrezIds. > I'm trying to perfom an hyperGTest and I want to restrict the > annotation to my subset of GO ids. > > So, I define a GOHyperGParams object (I use the slot "catogrySubsetIds" > to restrict to my GO Ids) > >>params = new ("GOHyperGParams",geneIds = genes, universeGeneIds = > > univers, annotation = "hgu133a", cateogrySubsetIds = GOBPselec) > > where GOBPselec is a vector of GO Ids : > >>GOBPselec > > [1] "GO:0006915" "GO:0007165" "GO:0006468" "GO:0006350" "GO:0006508" > "GO:0008152" "GO:0000004" "GO:0006355" "GO:0006457" "GO:0007242" > "GO:0006512" ...... > > And finally, I launch the test and I have the following error : > >>hg = hyperGTest(params) > > "Error in getGoToProbeMap(go2allprobes, ontology) : > incorrect type of index" > > I know that this error come from "cateogrySubsetIds" but I don't > understand why? I don't think it comes from cateogrySubsetIds, but from the fact that you aren't passing anything in for the 'ontology' slot. Try adding an ontology = "BP" to your call to new("GOHyperGParams", ...). Best, Jim > The description of this slot is : <<object of="" class="" "any":="" if="" the=""> test method supports it, can be used to specify a subset of category > ids to include in the test instead of all possible category ids. >> > > Best regards, > Anne. > > > > > > > > [[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 -- James W. MacDonald, M.S. Biostatistician Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues.

ADD REPLY • link 18.1 years ago Anne.Biton@sanofi-aventis.com ▴ 20

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Hi Anne, Anne.Biton at sanofi-aventis.com wrote: > Thanks James, (sorry for the stupid error!) No problem. I make at least one per day ;-D > In fact, now I return to my first problem : the slot catogrySubsetIds isn't taken into account : the annotation seems to be done on all GO Ids in the two cases : > > >>params = new ("GOHyperGParams",geneIds = genes, universeGeneIds = univers, annotation = "hgu133a", ontology = "BP") >>hgtest = hyperGTest(params) >>params = new ("GOHyperGParams",geneIds = genes, universeGeneIds = univers, annotation = "hgu133a", ontology = "BP",cateogrySubsetIds = GOBPselec) >>hgtest2 = hyperGTest(params) >>hgtest2 > > Gene to GO BP test for over-representation > 566 GO BP ids tested (11 have p < 0.01) > Selected gene set size: 155 > Gene universe size: 7620 > Annotation package: hgu133a > >>hgtest > > Gene to GO BP test for over-representation > 566 GO BP ids tested (11 have p < 0.01) > Selected gene set size: 155 > Gene universe size: 7620 > Annotation package: hgu133a As you already noted, the man page states 'cateogrySubsetIds': Object of class '"ANY"': If the test method supports it, can be used to specify a subset of category ids to include in the test instead of all possible category ids. I don't know which test method supports this argument, but apparently hyperGTest() doesn't. Best, Jim > > Best, > > Anne. > -- James W. MacDonald, M.S. Biostatistician Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues.

ADD REPLY • link 18.1 years ago James W. MacDonald 68k

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