[BioC] BiomaRt error when trying to get exon location info

[Daniel Brewer]

Hello,

I am trying to get all the exon location information from Ensembl using
biomaRt but I am running into problems.

library("biomaRt")
human=useMart("ensembl", dataset="hsapiens_gene_ensembl")
att <- c("ensembl_gene_id", "ensembl_transcript_id", "exon_chrom_start",
"exon_chrom_end", "rank", "phase", "ensembl_exon_id", "chromosome_name",
"external_gene_id", "strand")
yoda2 <- getBM(attributes=att,mart=human)

This results in:
Error in postForm(paste(martHost(mart), "?", sep = ""), query = xmlQuery) :
  Empty reply from server

I have also tried this:

library("biomaRt")
human=useMart("ensembl", dataset="hsapiens_gene_ensembl")
att <- c("ensembl_gene_id", "ensembl_transcript_id", "exon_chrom_start",
"exon_chrom_end", "rank", "phase", "ensembl_exon_id", "chromosome_name",
"external_gene_id", "strand")
yoda <- getBM(attributes="ensembl_transcript_id",mart=human)
yoda2 <- getBM(attributes=att,filters = "ensembl_transcript_id",
values=yoda, mart=human)

but get the same result.

The thing is that it really should be able to do this as I have managed
to so the same using emsembl's biomart web interface using the exact
same attributes.

Thanks

Dan

> sessionInfo()
R version 2.8.1 (2008-12-22)
x86_64-pc-linux-gnu

locale:
LC_CTYPE=en_GB.UTF-8;LC_NUMERIC=C;LC_TIME=en_GB.UTF-8;LC_COLLATE=en_GB.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_GB.UTF-8;LC_PAPER=en_GB.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_GB.UTF-8;LC_IDENTIFICATION=C

attached base packages:
[1] tools     stats     graphics  grDevices utils     datasets  methods
[8] base

other attached packages:
[1] Biobase_2.2.1  biomaRt_1.16.0

loaded via a namespace (and not attached):
[1] RCurl_0.93-0 XML_1.99-0


-- 
**************************************************************
Daniel Brewer, Ph.D.

Institute of Cancer Research
Molecular Carcinogenesis
Email: daniel.brewer at icr.ac.uk
**************************************************************

The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company Limited by Guarantee, Registered in England under Company No. 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP.

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