dear all, i am trying to build up an annotation package for a cDNA custom platform using ABPkgBuilder() based on EntrezGene IDs. the problem is that no probe is mapped in the "CHR" slot. my base file is (first 20 rows of 32447): 1_spt 22932 10_spt 5575 100_spt 2260 1000_spt 124540 10000_spt 23768 10001_spt 5288 10002_spt 434 10003_spt 586 10004_spt 26221 10005_spt 5551 10006_spt 909 10007_spt 10817 10008_spt 4004 10009_spt NA 1001_spt 57484 10010_spt 202 10011_spt NA 10012_spt 538 10013_spt 2050 10014_spt 1360 my URLs are: x<-getSrcUrl("all", organism="Homo sapiens") my QC output is: E5annEGQC [1] "\n\nQuality control information for E5annEG \nDate built: Created: Fri Aug 4 11:47:40 2006 \n \nNumber of probes: 32448 \nProbe number missmatch: None \ nProbe missmatch: None \nMappings found for probe based rda files: \n\t E5annEGA CCNUM found 0 of 32448\n\t E5annEGCHRLOC found 27954 of 32448\n\t E5annEGCHR fou nd 0 of 32448\n\t E5annEGENZYME found 3740 of 32448\n\t E5annEGGENENAME found 0 of 32448\n\t E5annEGLOCUSID found 29426 of 32448\n\t E5annEGMAP found 0 of 32448 \n\t E5annEGOMIM found 0 of 32448\n\t E5annEGPATH found 7620 of 32448\n\t E5annE GPMID found 0 of 32448\n\t E5annEGREFSEQ found 0 of 32448\n\t E5annEGSYMBOL foun d 0 of 32448\n\t E5annEGUNIGENE found 0 of 32448 \nMappings found for non-probe based rda files:\n \t E5annEGCHRLENGTHS found 25\n\t E5annEGENZYME2PROBE found 6 24\n\t E5annEGORGANISM found 1\n\t E5annEGPATH2PROBE found 178\n\t E5annEGPFAM f ound 22380\n\t E5annEGPROSITE found 15130 \n\n" sessionInfo(): attached base packages: [1] "tools" "methods" "stats" "graphics" "grDevices" "utils" [7] "datasets" "base" other attached packages: GO AnnBuilder RSQLite DBI annotate XML Biobase "1.10.0" "1.11.4" "0.4-1" "0.1-10" "1.10.0" "0.99-7" "1.10.0" do you have any suggestion? thanks for your help! sincerely Dario -- Dario Greco Institute of Biotechnology - University of Helsinki Building Cultivator II P.O.Box 56 Viikinkaari 4 FIN-00014 Finland Office: +358 9 191 58951 Fax: +358 9 191 58952 Mobile: +358 44 023 5780 Lab WebPage: http://www.biocenter.helsinki.fi/bi/dna-microarray/ Personal WebPage: http://www.biocenter.helsinki.fi/bi/dna- microarray/dario.htm

Dear Dario, Please upgrade AnnBuilder to 1.11.6 and rebuild your package with this script: library(AnnBuilder) mypkg <- function(pkgPath, version) { ABPkgBuilder(baseName="mybase.txt", baseMapType="ll", pkgName="mypkg", pkgPath=pkgPath, organism="Homo sapiens", version=version, author=list( authors="Dario Greco", maintainer="Dario Greco <email at="" email.com="">" ) ) } mypkg(getwd(), "1.0.0") Here is the result I got by using your sample baseFile: Quality control information for mypkg Date built: Created: Mon Aug 7 09:17:36 2006 Number of probes: 20 Probe number missmatch: None Probe missmatch: None Mappings found for probe based rda files: mypkgACCNUM found 0 of 20 mypkgCHRLOC found 18 of 20 mypkgCHR found 18 of 20 mypkgENZYME found 4 of 20 mypkgGENENAME found 18 of 20 mypkgGO found 16 of 20 mypkgLOCUSID found 18 of 20 mypkgMAP found 18 of 20 mypkgOMIM found 16 of 20 mypkgPATH found 7 of 20 mypkgPMID found 18 of 20 mypkgREFSEQ found 18 of 20 mypkgSUMFUNC found 0 of 20 mypkgSYMBOL found 18 of 20 mypkgUNIGENE found 18 of 20 Mappings found for non-probe based rda files: mypkgCHRLENGTHS found 25 mypkgENZYME2PROBE found 3 mypkgGO2ALLPROBES found 274 mypkgGO2PROBE found 89 mypkgORGANISM found 1 mypkgPATH2PROBE found 13 mypkgPFAM found 16 mypkgPMID2PROBE found 349 mypkgPROSITE found 14 mget(ls(mypkgCHR), mypkgCHR) $`10000_spt` [1] "14" $`10001_spt` [1] "12" $`10002_spt` [1] "20" $`10003_spt` [1] "12" $`10004_spt` [1] "22" $`10005_spt` [1] "10" $`10006_spt` [1] "1" $`10007_spt` [1] "6" $`10008_spt` [1] "11" $`10009_spt` [1] NA $`1000_spt` [1] "17" $`10010_spt` [1] "6" $`10011_spt` [1] NA $`10012_spt` [1] "X" $`10013_spt` [1] "7" $`10014_spt` [1] "3" $`1001_spt` [1] "4" $`100_spt` [1] "8" $`10_spt` [1] "7" $`1_spt` [1] "7" Hope it is helpful. Thanks nianhua