Question: KEGGHyperGParams variable "mouse4302PATH2EG" was not found
0
gravatar for John Coulthard
10.6 years ago by
John Coulthard170 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_US.u tf8;LC_MONETARY=C;LC_MESSAGES=en_US.utf8;LC_PAPER=en_US.utf8;LC_NAME=C ;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.utf8;LC_IDENTIFICATI ON=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]]
ADD COMMENTlink modified 10.6 years ago by Marc Carlson7.2k • written 10.6 years ago by John Coulthard170
Answer: KEGGHyperGParams variable "mouse4302PATH2EG" was not found
0
gravatar for Tony Chiang
10.6 years ago by
Tony Chiang570
Tony Chiang570 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@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_US .utf8;LC_MONETARY=C;LC_MESSAGES=en_US.utf8;LC_PAPER=en_US.utf8;LC_NAME =C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.utf8;LC_IDENTIFICA TION=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@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]]
ADD COMMENTlink written 10.6 years ago by Tony Chiang570
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 > >
ADD REPLYlink written 10.6 years ago by Marc Carlson7.2k
Answer: KEGGHyperGParams variable "mouse4302PATH2EG" was not found
0
gravatar for Marc Carlson
10.6 years ago by
Marc Carlson7.2k
United States
Marc Carlson7.2k wrote:
Hi John, At least part of your trouble is caused by an old bug that does not exist in modern versions of Bioconductor. Your problem should clear up if you simply update the Category package, but for best results I would encourage you to install the newest 2.9 release of R and the more recent 2.4 release of Bioconductor. At a bare minimum you should do this: source("http://bioconductor.org/biocLite.R") biocLite("Category") Which should at least update Category to version 2.8.4. Please let us know if you have any more questions. Marc John Coulthard 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_US .utf8;LC_MONETARY=C;LC_MESSAGES=en_US.utf8;LC_PAPER=en_US.utf8;LC_NAME =C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.utf8;LC_IDENTIFICA TION=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 > >
ADD COMMENTlink written 10.6 years ago by Marc Carlson7.2k
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