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

[steffen at stat.Berkeley.EDU]

Hi Daniel,

Try to do it chromosome by chromosome, it is a lot of information at once
that you're trying to retrieve.

This works for me:

> yoda2 <-
getBM(attributes=att,filters="chromosome_name",values=21,mart=human)
> yoda2[1,]
  ensembl_gene_id ensembl_transcript_id exon_chrom_start exon_chrom_end
rank phase
1 ENSG00000200792       ENST00000363922         32671367       32671502   
1    -1
  ensembl_exon_id chromosome_name external_gene_id strand
1 ENSE00001438685              21          SNORA42     -1


Cheers,
Steffen

> 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.
>
> This e-mail message is confidential and for use by the a...{{dropped:2}}
>
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