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

[Daniel Brewer]

Hi,

Thanks for the example, but that doesn't seem to work for me.

> 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,filters = "chromosome_name", values=21,
mart=human)

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

So it seems there is another problem.  I am running biomaRt_1.16.0.  Can
you tell me which version of biomaRt you are working with and if the
above coed is working?

Many thanks

Dan

steffen at stat.Berkeley.EDU wrote:
> 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
MUCRC
15 Cotswold Road
Sutton, Surrey SM2 5NG
United Kingdom

Tel: +44 (0) 20 8722 4109

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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