Hi Mark,

The default biomart.org server is extremely slow for me too (although I do
eventually get a result rather tha the network error HTML page you appear to
be getting).  Perhaps try the ensembl server instead:

mart <- useMart("ENSEMBL_MART_ENSEMBL", dataset="hsapiens_gene_ensembl",
host = "www.ensembl.org")

I get a much quicker response from that server.

Using your code I still don't get any exons, but swaping out <chromosome =
"chr1"> and using <chromosome = 1> seems to do the job nicely.

--
Mike Smith
PhD Student
Computational Biology Group
Cambridge University


On Tue, Nov 9, 2010 at 10:39 AM, Mark Dunning <mark.dunning@gmail.com>wrote:

> Hi all,
>
> I am trying to use the makeGeneRegion function in GenomeGraphs to get
> the locations of exons within a particular genomic region. The
> function seems to take an extraordinarily long time and then returns
> an error.
>
>
> >mart  = useMart("ensembl", dataset="hsapiens_gene_ensembl")
> >makeGeneRegion(start = 25592138, end = 25662215, chromosome = "chr1",
> strand="+", biomart=mart)
>
>
>
>          V1
> 1
> <HTML><HEAD>
> 2                                                      <TITLE>Network
> Error</TITLE>
> 3
>     </HEAD>
> 4
>      <BODY>
> 5 <table border="0" width="100%" cellspacing="0" cellpadding="0"
> bgcolor="#003399">
> 6
>        <tr>
> Error in getBM(c("ensembl_gene_id", "ensembl_transcript_id",
> "ensembl_exon_id",  :
>  The query to the BioMart webservice returned an invalid result: the
> number of columns in the result table does not equal the number of
> attributes in the query. Please report this to the mailing list.
>
>
>
> As it happens, I know that the region corresponds to the gene RHD and
> the following works as expected.
>
> > makeGene(id="RHD", type="hgnc_symbol", biomart=mart)
>  ID:RHD
>  Type:hgnc_symbol
>  Exons in Ensembl:
>  ensembl_gene_id ensembl_transcript_id ensembl_exon_id exon_chrom_start
> 1 ENSG00000187010       ENST00000328664 ENSE00001463282         25598981
> 2 ENSG00000187010       ENST00000328664 ENSE00001799547         25611064
> 3 ENSG00000187010       ENST00000328664 ENSE00001784803         25617132
> 4 ENSG00000187010       ENST00000328664 ENSE00001626654         25627437
> 5 ENSG00000187010       ENST00000328664 ENSE00001730743         25628011
>  exon_chrom_end rank strand        biotype
> 1       25599186    1      1 protein_coding
> 2       25611250    2      1 protein_coding
> 3       25617282    3      1 protein_coding
> 4       25627584    4      1 protein_coding
> 5       25628177    5      1 protein_coding
>
>
> Can anyone suggest why makeGeneRegion isn't behaving?
>
> Regards,
>
> Mark
>
>
>
> > sessionInfo()
> R version 2.12.0 (2010-10-15)
> Platform: x86_64-unknown-linux-gnu (64-bit)
>
> locale:
>  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
>  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
>  [5] LC_MONETARY=C              LC_MESSAGES=en_US.UTF-8
>  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
>  [9] LC_ADDRESS=C               LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] grid      stats     graphics  grDevices utils     datasets  methods
> [8] base
>
> other attached packages:
> [1] diagram_1.5           shape_1.2.2           GenomeGraphs_1.8.0
> [4] biomaRt_2.4.0         Rsamtools_1.2.0       Biostrings_2.17.26
> [7] GenomicFeatures_1.2.1 GenomicRanges_1.2.1   IRanges_1.8.2
>
> loaded via a namespace (and not attached):
> [1] Biobase_2.8.0      BSgenome_1.16.5    DBI_0.2-5          RCurl_1.4-3
> [5] RSQLite_0.9-2      rtracklayer_1.10.4 tools_2.12.0       XML_3.2-0
>
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