Dear List, I have some problem with goTools analysis and I hope yet again the great experts will help me. I have a list of significant genes and I am trying to use them for GO analysis using go bioc goTools package. sigGenes<- Illumina nuID( lumi package) obtained by adjusted p.value filtering. goIds<- getGO(sigGenes,"lumiHumanAll.db") probeType<- "GO" ontology<- "BP" ontoCompare(list(goIds),probeType = probeType, ontology = ontology, plot = TRUE) Starting ontoCompare... Error in goidvect[test] : invalid subscript type 'list' What I understand , the reason behind this is, getGO() method returns more than one GO Ids and terms for each nuID instead of returning a single GO ID for each nuID. Is there any way I can resolve this.....??? Thanks in advance regards, Mamun --------------------------------------------------- sessionInfo() R version 2.10.1 (2009-12-14) x86_64-unknown-linux-gnu locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] goProfiles_1.8.0 Biobase_2.6.1 [3] session_1.0.2 gtools_2.6.1 [5] limma_3.2.1 car_1.2-16 [7] hopach_2.6.0 cluster_1.12.1 [9] xtable_1.5-6 illuminaHumanv3BeadID.db_1.4.1 [11] Cairo_1.4-5 goTools_1.20.0 [13] GO.db_2.3.5 GOstats_2.12.0 [15] graph_1.24.1 Category_2.12.0 [17] lumiHumanIDMapping_1.4.0 lumiHumanAll.db_1.8.1 [19] org.Hs.eg.db_2.3.6 RSQLite_0.8-0 [21] DBI_0.2-5 preprocessCore_1.8.0 [23] annotate_1.24.0 AnnotationDbi_1.8.1 loaded via a namespace (and not attached): [1] affy_1.24.2 affyio_1.14.0 genefilter_1.28.2 grid_2.10.1 [5] GSEABase_1.8.0 lattice_0.17-26 lumi_1.12.2 MASS_7.3-4 [9] Matrix_0.999375-33 mgcv_1.6-1 nlme_3.1-96 RBGL_1.22.0 [13] splines_2.10.1 survival_2.35-7 tools_2.10.1 XML_2.6-0 >