First up want a great library, incredibly useful. thanks!

But I'm just a little confused by GenomicFeatures.Hsapiens.UCSC.hg18 and
GenomicFeatures.Mmusculus.UCSC.mm9 .

that is 
library(GenomicFeatures)
library(GenomicFeatures.Mmusculus.UCSC.mm9)
library(GenomicFeatures.Hsapiens.UCSC.hg18)


>   txdb <- loadFeatures(system.file("extdata",
"UCSC_knownGene_sample.sqlite",
package="GenomicFeatures",lib.loc="/home/pleo/R_latest/library")) ## NO
problem
>   txdb <-
loadFeatures(system.file("extdata","GenomicFeatures.Mmusculus.UCSC.mm9.sqlite", package="GenomicFeatures.Mmusculus.UCSC.mm9",lib.loc="/home/pleo/R_latest/library") )
Error in validObject(.Object) : 
  invalid class "TranscriptDb" object: the DB has no metadata table 
>   txdb <-
loadFeatures(system.file("extdata","GenomicFeatures.Hsapiens.UCSC.hg18.sqlite", package="GenomicFeatures.Hsapiens.UCSC.hg18",lib.loc="/home/pleo/R_latest/library") )
Error in validObject(.Object) : 
  invalid class 

Otherwise they usable by the geneHuman() or geneMouse() functions...

But I'm not sure what the missing meta table is about: how to the
GenomicFeatures.Mmusculus.UCSC.mm9 etc differ from the example
GenomicFeaures sql used as GenomicFeature example files (in the first)
line
Also what is the motivation fro putting them in the Experimental Data
section are you thinking these won't be supported/updated  by Biocore
Data team in the future?

Thanks
Paul


> sessionInfo()
R version 2.11.0 Under development (unstable) (2010-03-23 r51373) 
x86_64-unknown-linux-gnu 

locale:
 [1] LC_CTYPE=en_AU.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_AU.UTF-8        LC_COLLATE=en_AU.UTF-8    
 [5] LC_MONETARY=C              LC_MESSAGES=en_AU.UTF-8   
 [7] LC_PAPER=en_AU.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_AU.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] GenomicFeatures.Hsapiens.UCSC.hg18_0.1.2
 [2] org.Mm.eg.db_2.4.0                      
 [3] RSQLite_0.8-4                           
 [4] DBI_0.2-5                               
 [5] AnnotationDbi_1.9.6                     
 [6] Biobase_2.7.5                           
 [7] GenomicFeatures.Mmusculus.UCSC.mm9_0.1.2
 [8] GenomicFeatures_0.4.4                   
 [9] GenomicRanges_0.0.9                     
[10] IRanges_1.5.69                          

loaded via a namespace (and not attached):
[1] biomaRt_2.3.4      Biostrings_2.15.25 BSgenome_1.15.16   RCurl_1.3-1       
[5] rtracklayer_1.7.11 tcltk_2.11.0       tools_2.11.0       XML_2.8-1         
> 




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