Related to Tonys observation, you might find the GOstats vignette on Hypergeometric testing to be a helpful resource: http://www.bioconductor.org/packages/2.4/bioc/html/GOstats.html Marc Tony Chiang wrote: > Hi John, > > Is there any specific reason why your universeGeneIds is an empty character > vector? I think that might have something to do with things not working out > quite as you would think. > > tony > > On Wed, May 6, 2009 at 8:57 AM, John Coulthard <bahhab at="" hotmail.com=""> wrote: > > >> Hi >> >> Could someone please help me out with this error on a hyperGTest with KEGG >> parameters? I get the same error on the hgu133plus2 chip. Must be something >> wrong with my parameter definition but I can't work out what. >> >> >>> params<-new("KEGGHyperGParams", geneIds =entrez_set0.05, >>> >> universeGeneIds = character(0), annotation = "mouse4302", testDirection >> ="over") >> >> >>> hgkegg<- hyperGTest(params) >>> >> Error in get(paste(lib, name, sep = "")) : >> >> variable "mouse4302PATH2EG" was not found >> >> More details below. >> Many thanks >> John >> >> >> >>> class(entrez_set0.05) >>> >> [1] "character" >> >>> head(entrez_set0.05) >>> >> [1] "2673" "3977" "687" "54510" "51101" "6926" >> >>> ls("package:mouse4302.db") >>> >> [1] "mouse4302" "mouse4302ACCNUM" >> "mouse4302ALIAS2PROBE" >> [4] "mouse4302CHR" "mouse4302CHRLENGTHS" "mouse4302CHRLOC" >> [7] "mouse4302CHRLOCEND" "mouse4302_dbconn" "mouse4302_dbfile" >> [10] "mouse4302_dbInfo" "mouse4302_dbschema" "mouse4302ENSEMBL" >> [13] "mouse4302ENSEMBL2PROBE" "mouse4302ENTREZID" "mouse4302ENZYME" >> [16] "mouse4302ENZYME2PROBE" "mouse4302GENENAME" "mouse4302GO" >> [19] "mouse4302GO2ALLPROBES" "mouse4302GO2PROBE" "mouse4302MAP" >> [22] "mouse4302MAPCOUNTS" "mouse4302MGI" "mouse4302MGI2PROBE" >> [25] "mouse4302ORGANISM" "mouse4302PATH" >> "mouse4302PATH2PROBE" >> [28] "mouse4302PFAM" "mouse4302PMID" >> "mouse4302PMID2PROBE" >> [31] "mouse4302PROSITE" "mouse4302REFSEQ" "mouse4302SYMBOL" >> [34] "mouse4302UNIGENE" "mouse4302UNIPROT" >> >>> params<-new("KEGGHyperGParams", geneIds =entrez_set0.05, universeGeneIds >>> >> = character(0), annotation = "mouse4302", testDirection ="over") >> >>> hgkegg<- hyperGTest(params) >>> >> Error in get(paste(lib, name, sep = "")) : >> variable "mouse4302PATH2EG" was not found >> >> >>> sessionInfo() >>> >> R version 2.8.0 (2008-10-20) >> i386-redhat-linux-gnu >> >> locale: >> >> LC_CTYPE=en_US.utf8;LC_NUMERIC=C;LC_TIME=en_US.utf8;LC_COLLATE=en_U S.utf8;LC_MONETARY=C;LC_MESSAGES=en_US.utf8;LC_PAPER=en_US.utf8;LC_NAM E=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.utf8;LC_IDENTIFIC ATION=C >> >> attached base packages: >> [1] splines tools stats graphics grDevices utils datasets >> [8] methods base >> >> other attached packages: >> [1] gtools_2.5.0 GOstats_2.8.0 Category_2.8.3 >> [4] genefilter_1.22.0 survival_2.34-1 RBGL_1.18.0 >> [7] annotate_1.20.1 xtable_1.5-5 GO.db_2.2.5 >> [10] graph_1.20.0 RMySQL_0.7-2 KEGG.db_2.2.5 >> [13] mouse4302.db_2.2.5 moe430b.db_2.2.5 RSQLite_0.7-1 >> [16] DBI_0.2-4 AnnotationDbi_1.4.2 Biobase_2.2.2 >> >> loaded via a namespace (and not attached): >> [1] cluster_1.11.11 GSEABase_1.4.0 XML_1.98-1 >> >> >> _________________________________________________________________ >> [[elided Hotmail spam]] >> >> [[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 >> >> > > [[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 > >