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;L C_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_GB.UTF-8;LC_IDE NTIFICATION=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. This e-mail message is confidential and for use by the a...{{dropped:2}}