Scott, Gene symbols and other IDs are case sensitive. For mouse and rat, most OFFICIAL gene symbols are initial upper case only, while all upper cases for human and many other species. For example, some mappable gene symbols (from your list) for mouse would be like Cd74, Mgp and Cd52, while they should be CD74, MGP and CD52 for human. You may tried gene symbol search at NCBI like http://www.ncbi.nlm.nih.gov/gene/?term=CD52 and look at the results for different species. Weijun -------------------------------------------- On Thu, 1/9/14, Scott wrote: Subject: R pathview and mouse Date: Thursday, January 9, 2014, 4:41 PM Hello Weijun, I am trying to map mouse gene names to entrez ids using the id2eg in your path view tool.? Below shows what I did.? The variable ?T? holds the data, and I do a map, but none of the genes get mapped to entrez gene ids.? However, if I use human (?Hs?) then it works.? Do you know what is wrong? > biocLite("org.Mm.eg.db") > T ? ? ? H2-AB1? ? ???HSP105? ? ? ???CD74? ? ? ???GP38? ? ? ? ? MGP? ? ? ???CD52? ???TMEM176B? ? ? ? IFI27? ? ???LAPTM5? ? ? ? TGFBI? ???HSP90AB1 ? ? 3.880227? ???3.429302? ???3.417246? ???3.164127? ???2.932691? ???2.852793? ???2.665297? ???2.564207? ???2.534474? ???2.366048? ???2.301527 > T.id.map <- id2eg(ids = names(T), category = gene.idtype.list[1], org = "Mm") > T.id.map ? ? ? SYMBOL? ? ? ???EntrezGene [1,] "H2-AB1"? ? ???""? ? ? ? [2,] "HSP105"? ? ???""? ? ? ? [3,] "CD74"? ? ? ???""? ? ? ? [4,] "GP38"? ? ? ???""? ? ? ? [5,] "MGP"? ? ? ? ? ""? ? ? ? [6,] "CD52"? ? ? ???""? ? ? ? [7,] "TMEM176B"? ???""? ? ? ? [8,] "IFI27"? ? ? ? ""? ? ? ? [9,] "LAPTM5"? ? ???""? ? ? ? [10,] "TGFBI"? ? ? ? ""? ? ? ? [11,] "HSP90AB1"? ???""? ? ? ? However, if I use human then it works. > T.id.map <- id2eg(ids = names(T), category = gene.idtype.list[1], org = "Hs") > T.id.map ? ? ? SYMBOL? ? ? ???EntrezGene [1,] "H2-AB1"? ? ???""? ? ? ? [2,] "HSP105"? ? ???""? ? ? ? [3,] "CD74"? ? ? ???"972"? ??? [4,] "GP38"? ? ? ???""? ? ? ? [5,] "MGP"? ? ? ? ? "4256"? ? [6,] "CD52"? ? ? ???"1043"? ? [7,] "TMEM176B"? ???"28959"??? [8,] "IFI27"? ? ? ? "3429"? ? [9,] "LAPTM5"? ? ???"7805"? ? [10,] "TGFBI"? ? ? ? "7045"? ? [11,] "HSP90AB1"? ???"3326"? ? thanks Scott