Hello, 

I am trying to use goseq to find enriched GO terms for zebrafish RNA-seq data and am looking for advice on manually providing gene length information and GO annotation to goseq.    My RNA-Seq data is mapped to danRer7 Ensembl gene id's.   Unfortunately danRer7 does not appear to be supported by goeqs's built-ins for ensembl gene ids.

> supportedGenomes () [68,]
        db   species      date                  name AvailableGeneIDs
68 danRer7 Zebrafish Jul. 2010 Sanger Institute Zv9     

> pwf = nullp(gene.vector, "danRer7", "ensGene")
Error in getlength(names(DEgenes), genome, id) : 
  Length information for genome danRer7 and gene ID ensGene is not in the geneLenDataBase database.  You will have to specify bias.data manually.

I would like to manually supply the gene length information by:

> zv9txs = makeTranscriptDbFromBiomart (biomart ="ensembl", dataset = "drerio_gene_ensembl")
> txsByGene=transcriptsBy(zv9txs,"gene")
> lengthData=median(width(txsByGene))

and GO Data (using biomaRt):

> zv9 = useDataset("drerio_gene_ensembl",mart=useMart ("ensembl"))
> GOmap = getBM (filters = "ensembl_gene_id", attributes = c("ensembl_gene_id", "go_id"), values = gene.universe, mart = zv9)

How can I input this GO Data and gene length data into the nullp function of goseq to calculate a probability weighting function?

Thanks and sessionInfo() below, 

Ravi

> sessionInfo ()
R version 2.15.1 (2012-06-22)
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] GenomicFeatures_1.8.3  AnnotationDbi_1.18.1   Biobase_2.16.0         GenomicRanges_1.8.13  
 [5] IRanges_1.14.4         BiocGenerics_0.2.0     goseq_1.8.0            geneLenDataBase_0.99.9
 [9] BiasedUrn_1.04         biomaRt_2.12.0        

loaded via a namespace (and not attached):
 [1] Biostrings_2.24.1  bitops_1.0-4.1     BSgenome_1.24.0    DBI_0.2-5          grid_2.15.1       
 [6] hwriter_1.3        lattice_0.20-10    Matrix_1.0-6       mgcv_1.7-20        nlme_3.1-104      
[11] RCurl_1.91-1       Rsamtools_1.8.6    RSQLite_0.11.1     rtracklayer_1.16.3 ShortRead_1.14.4  
[16] stats4_2.15.1      tools_2.15.1       XML_3.9-4          zlibbioc_1.2.0    
> 
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