Hi Peter, Your input file looks OK at 1st glance. Are you trying to make an annotation package? Have you tried following the instructions in the vignette titled "SQLForge: An easy way to create a new annotation package with a standard database schema."? If not, you can read it here: http://www.bioconductor.org/packages/2.11/bioc/html/AnnotationForge.ht ml Marc On 03/30/2013 06:06 PM, Wang Peter wrote: > dear all : > i am using the input file primeviewHumanGeneExprs.txt > to creat an annotation file, such is the coding > source("http://bioconductor.org/biocLite.R"); > biocLite("human.db0"); > biocLite("AnnotationDbi"); > library(human.db0); > library(AnnotationDbi); > dir.create("primeview"); > > populateDB("HUMANCHIP_DB",affy=F,prefix="primeview",fileName="primev iewHumanGeneExprs.txt",metaDataSrc=c("DBSCHEMA"="HUMANCHIP_DB","ORGANI SM"="Homo > sapiens","SPECIES"="Human","MANUFACTURER"="Affymetrix","CHIPNAME"="P rimeView > Human Gene Expression Array","MANUFACTURERURL"="http://www.affymetrix.com > "),baseMapType="eg",outputDir="primeview"); > # > seed<-new("AnnDbPkgSeed",Package = > "primeview.db",Version="1.0.0",PkgTemplate="HUMANCHIP.DB",AnnObjPref ix="primeview"); > # > makeAnnDbPkg(seed,dbfile=file.path("primeview","primeview.sqlite"),d est_dir="primeview"); > > Error in makeAnnDbPkg(seed, file.path("primeview", "primeview.sqlite"), : > subscript out of bounds > >> sessionInfo() > R version 2.15.1 (2012-06-22) > Platform: x86_64-pc-mingw32/x64 (64-bit) > locale: > [1] LC_COLLATE=Chinese (Simplified)_People's Republic of China.936 > [2] LC_CTYPE=Chinese (Simplified)_People's Republic of China.936 > [3] LC_MONETARY=Chinese (Simplified)_People's Republic of China.936 > [4] LC_NUMERIC=C > [5] LC_TIME=Chinese (Simplified)_People's Republic of China.936 > attached base packages: > [1] stats graphics grDevices utils datasets methods base > other attached packages: > [1] RSQLite_0.11.2 DBI_0.2-5 human.db0_2.7.1 > [4] AnnotationDbi_1.18.4 Biobase_2.16.0 BiocGenerics_0.2.0 > loaded via a namespace (and not attached): > [1] IRanges_1.14.4 stats4_2.15.1 tools_2.15.1 > > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor [[alternative HTML version deleted]]