[BioC] makeTranscriptDbFromBiomart for Arabidopsis thaliana (plants_mart_10)

Wed Sep 21 16:23:18 CEST 2011

Hi Marc,

many thanks for your fast reply.

I managed to make it working by using another machine which has direct 
access to the internet (not via proxy).

---------------------------------------------
 > 
txdb_At<-makeTranscriptDbFromBiomart(biomart="plants_mart_10",dataset="athaliana_eg_gene")
Download and preprocess the 'transcripts' data frame ... OK
Download and preprocess the 'splicings' data frame ... OK
Download and preprocess the 'genes' data frame ... OK
Prepare the 'metadata' data frame ... OK
Make the TranscriptDb object ... OK
Warning messages:
1: In .normargSplicings(splicings, unique_tx_ids) :
   no CDS information for this TranscriptDb object
2: In .normargChrominfo(chrominfo, transcripts$tx_chrom, 
splicings$exon_chrom) :
   chromosome lengths and circularity flags are not available for this 
TranscriptDb object
 >
 > 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] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] GenomicFeatures_1.2.3 GenomicRanges_1.2.3   IRanges_1.8.9
[4] biomaRt_2.6.0         RCurl_1.6-10          bitops_1.0-4.1

loaded via a namespace (and not attached):
[1] Biobase_2.10.0     Biostrings_2.18.4  BSgenome_1.18.3    DBI_0.2-5
[5] RSQLite_0.9-4      rtracklayer_1.10.6 tools_2.12.0       XML_3.4-0
 >
---------------------------------------------

Best, Annaick

---
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