




Dear All,
 
How to create annotation package for not a supported (please see for available ones below) organism (e.g. D.magna: http://en.wikipedia.org/wiki/Daphnia_magna and other Crustaceans that are so important in environmental ecotoxicology/toxicogenomics)?

 What I have is a B2G annotation for probes arrayed on Agi4x44 chips.

As I know Biocore Data Team is responsible for the annotation packages. But how do the select organism to support?


Thanks
 
Alex
 
 
 References:
http://www.bioconductor.org/packages/2.6/bioc/vignettes/AnnotationDbi/inst/doc/SQLForge.pdf
http://www.bioconductor.org/packages/release/bioc/vignettes/AnnotationDbi/inst/doc/NewSchema.pdf


 
 
 
 >available.db0pkgs()
 [1] "anopheles.db0"   "arabidopsis.db0" "bovine.db0"      "canine.db0"      "chicken.db0"     "chimp.db0"       "ecoliK12.db0"    "ecoliSakai.db0" 
 [9] "fly.db0"         "human.db0"       "malaria.db0"     "mouse.db0"       "pig.db0"         "rat.db0"         "rhesus.db0"      "worm.db0"       
[17] "xenopus.db0"     "yeast.db0"       "zebrafish.db0" 


> sessionInfo()
R version 2.13.1 (2011-07-08)
Platform: i386-pc-mingw32/i386 (32-bit)

locale:
[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252    LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C                           LC_TIME=English_United States.1252    

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

other attached packages:
 [1] hgug4112a.db_2.5.0       org.Hs.eg.db_2.5.0       affycoretools_1.24.0     KEGG.db_2.5.0            GO.db_2.5.0              RSQLite_0.9-4           
 [7] DBI_0.2-5                affy_1.30.0              gplots_2.10.1            KernSmooth_2.23-6        caTools_1.12             bitops_1.0-4.1          
[13] gdata_2.8.2              gtools_2.6.2             marray_1.30.0            vsn_3.20.0               Agi4x44PreProcess_1.12.0 genefilter_1.34.0       
[19] annotate_1.30.1          AnnotationDbi_1.14.1     limma_3.8.3              Biobase_2.12.2          

loaded via a namespace (and not attached):
 [1] affyio_1.20.0         annaffy_1.24.0        biomaRt_2.8.1         Biostrings_2.20.3     Category_2.18.0       gcrma_2.24.1         
 [7] GOstats_2.18.0        graph_1.30.0          GSEABase_1.14.0       IRanges_1.10.6        lattice_0.19-30       preprocessCore_1.14.0
[13] RBGL_1.28.0           RCurl_1.6-10.1        splines_2.13.1        survival_2.36-9       tools_2.13.1          XML_3.4-2.2          
[19] xtable_1.5-6         



 


 

	[[alternative HTML version deleted]]

