I would go with @atpoint's second point above. I'm guessing that well-curated Rat references are pretty hard to come by.
If you're working with Ensembl gene IDs in your rat dataset, you can just do something like this:
ref <- MouseRNAseqData()
mart <- useMart("ensembl", dataset="mmusculus_gene_ensembl")
# Not the cleanest code, but whatever.
ens.mapping <- getBM(c("mgi_symbol", "ensembl_gene_id"), filters="mgi_symbol", values=rownames(ref), mart=mart)
homo.mapping <- getBM(c("ensembl_gene_id", "rnorvegicus_homolog_ensembl_gene"), filters="ensembl_gene_id",
mapping <- merge(ens.mapping, homo.mapping)
rat.genes <- mapping$rnorvegicus_homolog_ensembl_gene[match(rownames(ref), mapping$mgi_symbol)]
keep <- !is.na(rat.genes) & rat.genes!=""
rat.ref <- ref[keep,]
rownames(rat.ref) <- rat.genes[keep]
Same principle applies for the human celldex datasets - just swap
hgnc_symbol and replace
hsapiens. As usual, YMMV on cross-species comparisons, though hopefully the defining aspects of the major cell types are still preserved.