I am working with pig and got this error message when using goseq. I e-mailed with Nadia and she helped me find a solution to this so I thought I'd post it here in case anyone else run into the same problem.
It appears as though the pig gene ontology annotation package used by goseq (org.Ss.eg.db) doesn't support ensembl gene IDs so it is necessary to manually specify the GO terms, which can be done using biomart.
Here is the code:
library("biomaRt")
ensembl = useMart("ensembl",dataset="sscrofa_gene_ensembl")
groups=getBM(attributes=c("go_id","ensembl_gene_id"),filters="ensembl_gene_id",value=names(genes),mart=ensembl)
Then you can go on testing like this:
GO.wall=goseq(pwf,gene2cat=groups)
It appears as though the pig gene ontology annotation package used by goseq (org.Ss.eg.db) doesn't support ensembl gene IDs so it is necessary to manually specify the GO terms, which can be done using biomart.
Here is the code:
library("biomaRt")
ensembl = useMart("ensembl",dataset="sscrofa_gene_ensembl")
groups=getBM(attributes=c("go_id","ensembl_gene_id"),filters="ensembl_gene_id",value=names(genes),mart=ensembl)
Then you can go on testing like this:
GO.wall=goseq(pwf,gene2cat=groups)