Hi, There are 292 pathways according to pathway2gene, but there are 390 pathways according to pathway2name. I'm wondering why these two numbers are not the same. > library(KEGG.db) > pathway2gene=dbGetQuery(KEGG_dbconn(), "SELECT * FROM pathway2gene") > > species=unique(substr(unique(pathway2gene$pathway_id),1,3)) > species [1] "hsa" "ath" "dme" "mmu" "rno" "sce" "pfa" "dre" "eco" "ecs" "cfa" "bta" [13] "cel" "ssc" "gga" "mcc" "xla" "aga" "ptr" > > tmp=lapply( + species + , function(x) { + unique(pathway2gene$pathway_id[grep(paste('^', x,sep=''), pathway2gene$pathway_id)]) + } + ) > > sapply(tmp, length) [1] 229 123 127 225 225 99 80 155 105 107 224 225 125 225 152 225 150 126 225 > > tmp1=unique( + unlist( + lapply( + tmp + , function(x) { + substr(x, 4, 8) + } + ) + ) + ) > > length(tmp1) [1] 292 > pathway2name=dbGetQuery(KEGG_dbconn(), 'SELECT * FROM pathway2name') > length(unique(pathway2name$path_id)) [1] 390 > sessionInfo() R version 2.13.0 (2011-04-13) Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) locale: [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] stats graphics grDevices datasets utils methods base other attached packages: [1] smart.source_1.0 KEGG.db_2.5.0 RSQLite_0.9-4 [4] DBI_0.2-5 AnnotationDbi_1.14.1 Biobase_2.12.2 -- Regards, Peng