I'm using the biomaRt package in R to pull down ensembl annotations for a set of Affy probeIDs. The features seem nice, but the service is very slow, taking 10 minutes or so for a single query (of no more than a dozen probes), and frequently times out completely:
library('biomaRt') ensembl = useMart("ensembl") ensembl = useDataset("hsapiens_gene_ensembl",mart=ensembl) probePos = getBM(attributes=c("affy_huex_1_0_st_v2", "hgnc_symbol", "chromosome_name", "start_position", "end_position", "strand"), filters="affy_huex_1_0_st_v2", values=probeList, mart=ensembl)
The slow returns have persisted over a week or two, and don't seem dependent on time of day or anything like that. If I add a few more attributes, I get timeouts:
Request to BioMart web service failed. Verify if you are still connected to the internet. Alternatively the BioMart web service is temporarily down.
So, my questions are:
- Is this a common problem for others?
- Is likely that the server is overloaded, or are my queries just too big? If the former, are there any mirrors available?
- If the latter, the next step is setting up a local server, I guess. Anyone have experience (good or bad) with that? Is it worth the hassle?