[BioC] makeTranscriptDbFromBiomart for Arabidopsis thaliana (plants_mart_10)

Tue Sep 20 12:08:34 CEST 2011

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