[BioC] makeTranscriptDbFromBiomart for Arabidopsis thaliana (plants_mart_10)

Tue Sep 20 23:35:09 CEST 2011

Hi Annaick,

I was unable to reproduce your error.  My sessionInfo() (below), shows a 
very similar result to yours (only R looks different which is unlikely 
to cause this).  But biomaRt sometimes can be a little testy since it 
relies on a web-service.  So perhaps you should try again?

   Marc

 > sessionInfo()
R version 2.13.1 Patched (2011-08-25 r56798)
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] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] GenomicFeatures_1.4.4 GenomicRanges_1.4.8   IRanges_1.10.6

loaded via a namespace (and not attached):
[1] biomaRt_2.8.1      Biostrings_2.20.3  BSgenome_1.20.0    DBI_0.2-5
[5] RCurl_1.6-9        RSQLite_0.9-4      rtracklayer_1.12.4 tools_2.13.1
[9] XML_3.4-2

   Marc

On 09/20/2011 03:08 AM, annaick.carles wrote:
> Dear Bioconductor mailing list,
>
> i need to get the length of genes in Arabidopsis thaliana in order to 
> use the R package 'goseq'. Since Arabidopsis thaliana is not in the 
> native 'goseq' database, I first tried to get a 'transcriptDb' object 
> as suggested in the documentation of 'goseq', with 
> 'makeTranscriptDbFromBiomart' command from the 'GenomicFeatures' 
> package. But I got the following error message:
>
> -----------------------------------
> > 
> txdb_At<-makeTranscriptDbFromBiomart(biomart="plants_mart_10",dataset="athaliana_eg_gene")
> Download and preprocess the 'transcripts' data frame ...
>                                       V1
> 1 <!DOCTYPE HTML PUBLIC -//W3C//DTD HTML 4.01 Transitional//EN 
> http://www.w3.org/TR/html4/loose.dtd>
> 2 <HTML><HEAD><META HTTP-EQUIV=Content-Type CONTENT=text/html; 
> charset=iso-8859-1>
> 3 <TITLE>ERROR: The requested URL could not be retrieved</TITLE>
> 4 <STYLE 
> type=text/css><!--BODY{background-color:#ffffff;font-family:verdana,sans-serif}PRE{font-family:sans-serif}--></STYLE>
> 5 </HEAD><BODY>
> 6 <H1>ERROR</H1>
> Error in getBM(.A1_ATTRIBS, filters = filters, values = values, mart = 
> mart) :
>   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.
> >
> > sessionInfo()
> R version 2.13.0 (2011-04-13)
> Platform: i386-pc-mingw32/i386 (32-bit)
>
> locale:
> [1] LC_COLLATE=English_United Kingdom.1252  LC_CTYPE=English_United 
> Kingdom.1252    LC_MONETARY=English_United Kingdom.1252 LC_NUMERIC=C
> [5] LC_TIME=English_United Kingdom.1252
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
>  [1] org.At.tair.db_2.5.0   RSQLite_0.9-4          DBI_0.2-5 
> AnnotationDbi_1.14.1   Biobase_2.12.2         goseq_1.4.0 
> geneLenDataBase_0.99.7 BiasedUrn_1.04
>  [9] biomaRt_2.8.1          GenomicFeatures_1.4.4  GenomicRanges_1.4.8 
>    IRanges_1.10.6         rtracklayer_1.12.4     RCurl_1.6-10.1 
> bitops_1.0-4.1
>
> loaded via a namespace (and not attached):
> [1] Biostrings_2.20.3  BSgenome_1.20.0    grid_2.13.0 lattice_0.19-33 
>  Matrix_0.9996875-3 mgcv_1.7-6         nlme_3.1-102     tools_2.13.0 
>     XML_3.4-2.2
> >
> -----------------------------------
>
>
> Many thanks in advance for your help!
>
>
> Annaick Carles
> FRISYS Core Facility Data Management
> ZBSA - University of Freiburg
> Germany
>
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