Dear List, I am using your package "GOstats" for my gene expression data. I took seleceted gene id (entrez id) and gene universrse which is all gens in the chip we used (entrez id) form excel file provided by the genome studio software. Here is the code. If you have some available time I want to you to validate the code . setwd("W:/KAUSHAL_RESEARCH/K_Surendaran/Data") source("http://www.bioconductor.org/biocLite.R") biocLite("AnnotatidatonDbi") library("AnnotationDbi") biocLite("illuminaMousev2.db") library("illuminaMousev2.db") biocLite("GOstats") library("GOstats") biocLite("KEGG.db") library("KEGG.db") biocLite("reactome.db") library("reactome.db") data1=read.csv("uni_id.csv", header=T) ### gene universe data2=data.matrix(data1) colnames(data2)<-NULL AllID=as.numeric(data2) head(AllID) [1] 212772 212772 100039693 56378 74257 20510 data3=read.csv("selec_ID.csv", header=T) ### selected gene data4=data.matrix(data3) colnames(data4)<-NULL SelecID=as.numeric(data4) head(SelecID) [1] 74257 20322 59010 66398 50995 242864 getClass("GOHyperGParams") getClass("KEGGHyperGParams") params<-new("GOHyperGParams", geneIds=SelecID, universeGeneIds=AllID, annotation=c("illuminaMousev2"), ontology="BP", pvalueCutoff=0.01, testDirection="over") resultBP1<-hyperGTest(params) resultBP1 summary(resultBP1) htmlReport(resultBP1, file="ALL_hgo.html") Partial output: GOBPID Pvalue OddsRatio ExpCount Count Size Term GO:0001905 0.000 Inf 0 2 2 activation of membrane attack complex I also want to get the genes in the count column. Thank you very much for help. -- output of sessionInfo(): > sessionInfo() R version 3.0.1 (2013-05-16) Platform: x86_64-w64-mingw32/x64 (64-bit) locale: [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 [3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C [5] LC_TIME=English_United States.1252 attached base packages: [1] parallel stats graphics grDevices utils datasets methods base other attached packages: [1] xtable_1.7-1 GO.db_2.9.0 reactome.db_1.44.0 [4] KEGG.db_2.9.1 GOstats_2.26.0 graph_1.38.3 [7] Category_2.26.0 illuminaMousev2.db_1.18.0 org.Mm.eg.db_2.9.0 [10] RSQLite_0.11.4 DBI_0.2-7 AnnotationDbi_1.22.6 [13] Biobase_2.20.1 BiocGenerics_0.6.0 BiocInstaller_1.10.3 loaded via a namespace (and not attached): [1] annotate_1.38.0 AnnotationForge_1.2.2 genefilter_1.42.0 GSEABase_1.22.0 [5] IRanges_1.18.4 RBGL_1.36.2 splines_3.0.1 stats4_3.0.1 [9] survival_2.37-4 tools_3.0.1 XML_3.98-1.1 -- Sent via the guest posting facility at bioconductor.org.

On Monday, September 30, 2013 1:36:36 PM, kaushal Raj Chaudhary [guest] wrote: > > Dear List, > > I am using your package "GOstats" for my gene expression data. I took seleceted gene id (entrez id) and gene universrse which is all gens in the chip we used (entrez id) form excel file provided by the genome studio software. Here is the code. If you have some available time I want to you to validate the code . > > > > setwd("W:/KAUSHAL_RESEARCH/K_Surendaran/Data") > > source("http://www.bioconductor.org/biocLite.R") > > biocLite("AnnotatidatonDbi") > > library("AnnotationDbi") > > biocLite("illuminaMousev2.db") > > library("illuminaMousev2.db") > > biocLite("GOstats") > > library("GOstats") > > biocLite("KEGG.db") > > library("KEGG.db") > > biocLite("reactome.db") > > library("reactome.db") > > > > data1=read.csv("uni_id.csv", header=T) ### gene universe > > data2=data.matrix(data1) > > colnames(data2)<-NULL > > AllID=as.numeric(data2) > > head(AllID) > > > > [1] 212772 212772 100039693 56378 74257 20510 > > > data3=read.csv("selec_ID.csv", header=T) ### selected gene > > data4=data.matrix(data3) > > colnames(data4)<-NULL > > SelecID=as.numeric(data4) > > head(SelecID) > > > > [1] 74257 20322 59010 66398 50995 242864 > > > getClass("GOHyperGParams") > > getClass("KEGGHyperGParams") > > > > params<-new("GOHyperGParams", geneIds=SelecID, universeGeneIds=AllID, annotation=c("illuminaMousev2"), ontology="BP", pvalueCutoff=0.01, testDirection="over") > > resultBP1<-hyperGTest(params) > > resultBP1 > > summary(resultBP1) > > htmlReport(resultBP1, file="ALL_hgo.html") > > > > Partial output: > GOBPID Pvalue OddsRatio ExpCount Count Size Term > GO:0001905 0.000 Inf 0 2 2 activation of membrane attack complex > > > > I also want to get the genes in the count column. You can get those genes using probeSetSummary() Best, Jim > > Thank you very much for help. > > > > > -- output of sessionInfo(): > >> sessionInfo() > R version 3.0.1 (2013-05-16) > Platform: x86_64-w64-mingw32/x64 (64-bit) > > locale: > [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 > [3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C > [5] LC_TIME=English_United States.1252 > > attached base packages: > [1] parallel stats graphics grDevices utils datasets methods base > > other attached packages: > [1] xtable_1.7-1 GO.db_2.9.0 reactome.db_1.44.0 > [4] KEGG.db_2.9.1 GOstats_2.26.0 graph_1.38.3 > [7] Category_2.26.0 illuminaMousev2.db_1.18.0 org.Mm.eg.db_2.9.0 > [10] RSQLite_0.11.4 DBI_0.2-7 AnnotationDbi_1.22.6 > [13] Biobase_2.20.1 BiocGenerics_0.6.0 BiocInstaller_1.10.3 > > loaded via a namespace (and not attached): > [1] annotate_1.38.0 AnnotationForge_1.2.2 genefilter_1.42.0 GSEABase_1.22.0 > [5] IRanges_1.18.4 RBGL_1.36.2 splines_3.0.1 stats4_3.0.1 > [9] survival_2.37-4 tools_3.0.1 XML_3.98-1.1 > > -- > Sent via the guest posting facility at bioconductor.org. > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > 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 University of Washington Environmental and Occupational Health Sciences 4225 Roosevelt Way NE, # 100 Seattle WA 98105-6099

Thank you very much, James. I have to create the named vector for selected gene ids. Regards,