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.html


   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="primeviewHumanGeneExprs.txt",metaDataSrc=c("DBSCHEMA"="HUMANCHIP_DB","ORGANISM"="Homo
> sapiens","SPECIES"="Human","MANUFACTURER"="Affymetrix","CHIPNAME"="PrimeView
> 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",AnnObjPrefix="primeview");
> #
> makeAnnDbPkg(seed,dbfile=file.path("primeview","primeview.sqlite"),dest_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
>
>
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