Hello, Last time I got problem with basefile type of "ll" (Entrez Gene), and John and Nianhua fixed it quickly. And this time, I used basefile type of "refseq" or "gbNRef", because my base file mapping was based on Refseq IDs. I tried 2-column or 3-column base file. And I got package built, but a lot annotation data are missing, like Gene symbols, gene names, Unigene IDs, etc, and all the present annotation has no entries at all. My feeling is we might have some similar problems for Refseq IDs as last time for Entrez Gene IDs, but I am not positive about this. Please let me know if you have any ideas/suggestions. Thank you so much. Weijun The codes are almost the same as last time, except the difference related to base file. library(AnnBuilder) load('/Users/luow/project/microarraydata/annotation/hs95av2Refseq7.Rda ta') myBase=cbind(hs95av2Refseq7,hs95av2Refseq7) myBase[,2]=unlist(strsplit(myBase[,2],'_at')) write.table(myBase,file='/Users/luow/project/microarraydata/annotation /hs95av2Refseq7Base.txt',sep='\t',row.names=F,col.names=F) myBase='/Users/luow/project/microarraydata/annotation/hs95av2Refseq7Ba se.txt' myBaseType <-"refseq" #myBaseType <-"gbNRef" myDir <- '/Users/luow/project/microarraydata/annotation/' ABPkgBuilder(baseName = myBase, baseMapType = myBaseType, pkgName = "hs95av2Refseq7", 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/hs95av2Refse q7Base.txt',sep='\t',head=F)[100:110,] > a V1 V2 100 NM_000049_at NM_000049 101 NM_000050_at NM_000050 102 NM_000051_at NM_000051 103 NM_000053_at NM_000053 104 NM_000054_at NM_000054 105 NM_000055_at NM_000055 106 NM_000056_at NM_000056 107 NM_000057_at NM_000057 108 NM_000059_at NM_000059 109 NM_000060_at NM_000060 110 NM_000061_at NM_000061 > Here is what I got after I install the package > library(hs95av2Refseq7) > hs95av2Refseq7() Quality control information for hs95av2Refseq7 Date built: Created: Sun Jul 23 14:52:11 2006 Number of probes: 12548 Probe number missmatch: hs95av2Refseq7ACCNUM; hs95av2Refseq7CHRLOC; hs95av2Refseq7ENZYME; hs95av2Refseq7LOCUSID; hs95av2Refseq7PATH Probe missmatch: None Mappings found for probe based rda files: hs95av2Refseq7ACCNUM found 125485 of 12548 hs95av2Refseq7CHRLOC found 0 of 12548 hs95av2Refseq7ENZYME found 0 of 12548 hs95av2Refseq7LOCUSID found 0 of 12548 hs95av2Refseq7PATH found 0 of 12548 Mappings found for non-probe based rda files: hs95av2Refseq7CHRLENGTHS found 25 hs95av2Refseq7ORGANISM found 1 hs95av2Refseq7PFAM found 0 hs95av2Refseq7PROSITE found 0 Here is my environment, noticed that AnnBuilder 1.11.4 works fine with R 2.3.1, and I got good package built with base file mapping of Entrez Gene IDs under the same environment. > sessionInfo() Version 2.3.1 (2006-06-01) powerpc-apple-darwin8.6.0 attached base packages: [1] "tools" "methods" "stats" "graphics" "grDevices" "utils" [7] "datasets" "base" other attached packages: AnnBuilder RSQLite DBI annotate XML Biobase "1.11.4" "0.4-1" "0.1-10" "1.10.0" "0.99-7" "1.10.0" >