I usually use biomaRt to convert gene ids to symbols. However, this time the ensembl IDs I have (dog) do not match the ensembl ids of biomart dataset "clfamiliaris_gene_ensembl".
I also tried to use the ensembl web portal, the dog dataset is called ROS_Cfam_1.0 there. Looks like my genes do not match the genes from their dataset. My genes look like this:
"ENSCAFG00000045440" "ENSCAFG00000000001" "ENSCAFG00000000002" "ENSCAFG00000041462" "ENSCAFG00000000005"
Here is my biomaRt code:
ensembl <- useMart("ensembl") ensembl <- useDataset("clfamiliaris_gene_ensembl",mart=ensembl) gene_id <- getBM(attributes = c('ensembl_gene_id', 'external_gene_name'), values = rownames(mydata), filters = c('ensembl_gene_id'), mart = ensembl) gene_id  ensembl_gene_id external_gene_name <0 rows> (or 0-length row.names)
it doesn't find my values. Should I use a different dataset for dogs?