My guess is I just don't know what I am doing...
The following code worked well prior to December release:
mart <- useMart(biomart = "ENSEMBL_MART_ENSEMBL", dataset = "dmelanogaster_gene_ensembl", host = 'ensembl.org')
t2g <- getBM(attributes = c("ensembl_transcript_id", "ensembl_gene_id", "external_gene_name", "transcript_biotype"), mart = mart)
But now I have the following error:
Error in scan(file = file, what = what, sep = sep, quote = quote, dec = dec, : line 1 did not have 3 elements
I have tried 'useEnsembl' and specifying version 90 but that didn't seem to help. mart@host is always "http://e90.ensembl.org:80/biomart/martservice" unless I specify the host as "e91.ensembl.org" in my useMart code above. But I still get the same error regardless.
Is there something simple I am doing wrong?