Hi Nenad,

Thanks for reporting this.  I'll look into what is causing this.  Most
likely it is a bug at the Ensembl BioMart server side and not the biomaRt
package.

Cheers,
Steffen

On Thu, Jul 8, 2010 at 9:24 AM, Nenad Bartonicek <nenad@ebi.ac.uk> wrote:

> Hi,
>
> I would like to report a bug in biomaRt service.
> If I use the function getBM and I am searching for UTRs or coding
> sequence as well as identifiers, I get them in scrambled order.
> Meaning, the content of columns does not correspond to their headers:
>
> library(biomaRt)
> ensembl=useMart("ensembl", dataset="mmusculus_gene_ensembl")
> getBM
> (attributes
> =
> c
> ("ensembl_gene_id
> ","ensembl_transcript_id
> ","coding
> "),filters
> ="ensembl_gene_id",values=c("ENSMUSG00000028661"),mart=ensembl)
>
> This will result in something like:
>
>  ensembl_gene_id
>
>
> ATGGCCCCCGCCCGGGCCCGCCTGTCCCCCGCTCTCTGGGTCGTCACGGCCGCGGCGGCGGCCACCTGCGTGTCCGCGGGGCGCGGCGAAGTGAACTTGTTGGATACATCAACCATCCACGGAGACTGGGGCTGGCTCACGTATCCCGCTCATGGGTGGGACTCCATCAACGAGGTAGACGAGTCCTTCCGGCCCATCCACACGTACCA
> ....
>
> ensembl_transcript_id             coding
> ENSMUSG00000028661 ENSMUST00000030420
>
> Hope this helps somebody.
>
> Cheers,
>
> Nenad
>
> Nenad Bartonicek
> PhD student, Enright group
> European Bioinformatics Institute
> Hinxton
> Cambridge
> CB10 1SD
> United Kingdom
>
>
>  > sessionInfo()
> R version 2.11.0 (2010-04-22)
> x86_64-unknown-linux-gnu
>
> locale:
>  [1] LC_CTYPE=en_GB.UTF-8       LC_NUMERIC=C
>  [3] LC_TIME=en_GB.UTF-8        LC_COLLATE=en_GB.UTF-8
>  [5] LC_MONETARY=C              LC_MESSAGES=en_GB.UTF-8
>  [7] LC_PAPER=en_GB.UTF-8       LC_NAME=C
>  [9] LC_ADDRESS=C               LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats     graphics  grDevices datasets  utils     methods   base
>
> other attached packages:
>  [1] BSgenome_1.16.5     seqinr_2.0-9        RMySQL_0.7-4
>  [4] DBI_0.2-5           RColorBrewer_1.0-2  biomaRt_2.4.0
>  [7] ShortRead_1.6.2     Rsamtools_1.0.5     lattice_0.18-8
> [10] Biostrings_2.16.7   GenomicRanges_1.0.5 IRanges_1.6.8
> [13] R.utils_1.4.3       R.oo_1.7.3          R.methodsS3_1.2.0
>
> loaded via a namespace (and not attached):
> [1] Biobase_2.8.0 grid_2.11.0   hwriter_1.2   RCurl_1.4-2   tools_2.11.0
> [6] XML_3.1-0
>
>
>
>
>
>
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>
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