Hi Jim, There is an updated list of supported species in inst/NEWS file for the AnnotationDbi package. You can also just look for appropriate ".db0" files on offer at the web site the way that you could search for a platform specific package. Only the intermediate databases end with the ".db0" extension. http://www.bioconductor.org/packages/release/data/annotation/ Marc James W. MacDonald wrote: > Thanks, Marc. I know you recently posted on the listserv which species > have a .db0 file (and for which a annotation package can be built), > but is there somewhere that an updated list is posted of the available > species? > > Best, > > Jim > > > > Marc Carlson wrote: >> Hi guys, >> >> You could make a package using the SQLForge code in the AnnotationDbi >> package. Here is where you can find a vignette to explain how to use >> it: >> >> http://www.bioconductor.org/packages/release/bioc/html/AnnotationDb i.html >> >> >> Marc >> >> >> James W. MacDonald wrote: >>> Hi Minwook, >>> >>> Minwook Kim wrote: >>>> Hi, >>>> I run the aafTableAnn() to get the annotation information of eocli2. >>>> But I got the error. I did try to get the ecoli package. but it >>>> failed. Anyone help me? >>>>> AnnTable2 <- aafTableAnn(AllGenes,chiptype,AnnCols[2]); >>>> Loading required package: ecoli2 >>>> Error in aaf.handler(chip = chip) : Couldn't load data package ecoli2 >>>> In addition: Warning message: >>>> In library(package, lib.loc = lib.loc, character.only = TRUE, >>>> logical.return = TRUE, : >>>> there is no package called 'ecoli2' >>> This is true. In addition, there is no ecoli2.db package, nor can I >>> find any Biomart servers that might help. So for the time being, it >>> appears the best bet for annotation is the annotation file from >>> Affymetrix. >>> >>> http://www.affymetrix.com/Auth/analysis/downloads/na26/ivt/E_coli_ 2.na26.annot.csv.zip >>> >>> >>> >>> You can make HTML or text tables using this file and the annotate >>> package if that is what you are trying to do - see the 'Get HTML >>> Output' vignette. >>> >>> Best, >>> >>> Jim >>> >>> >>>> >>>> Apparently, the following information are helpful to fix it. >>>>> chiptype >>>> [1] "ecoli2" >>>> >>>> "AllGenes" variable includes probe ids. >>>> >>>> I guess "ecoli2" microarry is not supported by annaffy package. or I >>>> don"t know how to download the ecoli2 package. >>>> Thanks. >>>> Minwook >>>> >>>> >>>>> sessionInfo() >>>> R version 2.7.0 (2008-04-22) x86_64-redhat-linux-gnu locale: >>>> LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE= en_US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8 ;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_I DENTIFICATION=C >>>> >>>> >>>> attached base packages: >>>> [1] splines tools stats graphics grDevices utils >>>> datasets [8] methods base other attached packages: >>>> [1] gplots_2.6.0 gdata_2.4.2 gtools_2.5.0 >>>> [4] simpleaffy_2.16.1 ecoli2probe_2.2.0 ecoli2cdf_2.2.0 >>>> [7] bioDist_1.12.0 genefilter_1.20.1 survival_2.34-1 >>>> [10] annaffy_1.12.1 KEGG.db_2.2.0 GO.db_2.2.0 >>>> [13] AnnotationDbi_1.2.2 RSQLite_0.7-1 DBI_0.2-4 >>>> [16] gcrma_2.12.1 matchprobes_1.12.1 affy_1.18.2 >>>> [19] preprocessCore_1.2.1 affyio_1.8.1 Biobase_2.0.1 >>>> loaded via a namespace (and not attached): >>>> [1] annotate_1.18.0 >>>> >>>> >>>> >>>> >>>> _______________________________________________ >>>> Bioconductor mailing list >>>> Bioconductor at stat.math.ethz.ch >>>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>>> Search the archives: >>>> http://news.gmane.org/gmane.science.biology.informatics.conductor >> >

Hi Jim, James W. MacDonald wrote: > Thanks, Marc. I know you recently posted on the listserv which species > have a .db0 file (and for which a annotation package can be built), but > is there somewhere that an updated list is posted of the available species? Get the real-time availability with: available.db0pkgs <- function() { url <- "http://bioconductor.org/packages/release/data/annotation/src/contrib" pkgs <- available.packages(url)[, "Package"] pkgs <- pkgs[substr(pkgs, nchar(pkgs)-3, nchar(pkgs)) == ".db0"] names(pkgs) <- NULL pkgs } > available.db0pkgs() [1] "arabidopsis.db0" "bovine.db0" "canine.db0" "chicken.db0" [5] "ecoliK12.db0" "ecoliSakai.db0" "fly.db0" "human.db0" [9] "malaria.db0" "mouse.db0" "pig.db0" "rat.db0" [13] "worm.db0" "yeast.db0" "zebrafish.db0" Cheers, H.