Is anybody able to use the Bioconducter goseq package with mouse (mm9) gene id's?
It works fine when I use hg19 gene id's but when I switch to mouse it cannot find the database.
Below is the error I get:
> library(goseq)
> GO.wall=goseq(pwf, "mm9", "geneSymbol")
Fetching GO annotations...
Error in library(paste(orgstring, "db", sep = "."), character.only = TRUE) :
there is no package called ‘org.Gg.eg.db’
> sessionInfo()
R version 2.14.2 (2012-02-29)
Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] org.Hs.eg.db_2.6.4 RSQLite_0.11.1 DBI_0.2-5
[4] AnnotationDbi_1.16.19 Biobase_2.14.0 goseq_1.6.0
[7] geneLenDataBase_0.99.8 BiasedUrn_1.04
loaded via a namespace (and not attached):
[1] biomaRt_2.10.0 Biostrings_2.22.0 BSgenome_1.22.0
[4] GenomicFeatures_1.6.9 GenomicRanges_1.6.7 grid_2.14.2
[7] IRanges_1.12.6 lattice_0.20-6 Matrix_1.0-5
[10] mgcv_1.7-13 nlme_3.1-103 RCurl_1.91-1
[13] rtracklayer_1.14.4 tools_2.14.2 XML_3.9-4
[16] zlibbioc_1.0.1
Difficult to tell from your post, but you may need to install the appropriate genome annotation package; perhaps BSgenome.Mmusculus.UCSC.mm9? from Bioconductor.