Hello All, I posted this a couple of days ago, following some nice feedback. But haven't got further response yet, could anybody give me any suggestion/ideas on this problem? Thank you so much. BTW, I tried to update AnnBuilder package with biocLite('AnnBuilder') all I got is still the old version, AnnBuilder_1.10.0, I am not sure exactly how to get the updated version AnnBuilder_1.10.1, as suggested by Nianhua in an earlier message. Weijun ##older messages### Thank you so much, guys, For John??s question, My base map type is "ll", since my probes are mapped to Entrez Gene IDs directly. For Nianhua??s question, below is all my codes for this work. library(AnnBuilder) load('/Users/luow/project/microarraydata/annotation/hs95av2Entrezg7.Rd ata') myBase=cbind(hs95av2Entrezg7,hs95av2Entrezg7) myBase[,1]=paste(hs95av2Entrezg7,'_at',sep='') write.table(myBase,file='/Users/luow/project/microarraydata/annotation /hs95av2Entrezg7Base.txt',sep='\t',row.names=F,col.names=F) myBase='/Users/luow/project/microarraydata/annotation/hs95av2Entrezg7B ase.txt' myBaseType <- "ll" myDir <- '/Users/luow/project/microarraydata/annotation/' ABPkgBuilder(baseName = myBase, baseMapType = myBaseType, pkgName = "hs95av2Entrezg7", pkgPath = myDir, organism = "Homo sapiens", version = "1.1.0", author = list(authors = "Weijun", maintainer = "Weijun <luo_weijun at="" yahoo.com="">"), fromWeb =T) Here is part of my base file: > a=read.delim('/Users/luow/project/microarraydata/annotation/hs95av2Ent rezg7Base.txt',sep='\t', head=F) > head(a) V1 V2 1 10001_at 10001 2 10002_at 10002 3 10003_at 10003 4 10004_at 10004 5 10005_at 10005 6 10006_at 10006 Here is what I got when I created and installed the package. And Nianhua is right, I got problem with hs95av2Entrezg7CHRLOC environment, no entry at all. I will need to update my AnnBuilder. But exactly how can I do that, using update.packages function or, is there anything for updating bioc packages specially? > library(hs95av2Entrezg7) > hs95av2Entrezg7() Quality control information for hs95av2Entrezg7 Date built: Created: Sat Jul 8 20:23:41 2006 Number of probes: 8359 Probe number missmatch: None Probe missmatch: None Mappings found for probe based rda files: hs95av2Entrezg7CHRLOC found 0 of 8359 hs95av2Entrezg7ENZYME found 1313 of 8359 hs95av2Entrezg7LOCUSID found 8292 of 8359 hs95av2Entrezg7PATH found 2784 of 8359 Mappings found for non-probe based rda files: hs95av2Entrezg7CHRLENGTHS found 25 hs95av2Entrezg7ENZYME2PROBE found 651 hs95av2Entrezg7ORGANISM found 1 hs95av2Entrezg7PATH2PROBE found 180 hs95av2Entrezg7PFAM found 6997 hs95av2Entrezg7PROSITE found 5451 Please let me know if you have any ideas, suggestions, or other questions. I really appreciate all the kind help you guys offer! Weijun