[BioC] Error in BioMart and wormbase

[Vinuela, Ana]

Problem solved, 

Thank you Steffen. 

Ana.  


-----Original Message-----
From: steffen at stat.Berkeley.EDU [mailto:steffen at stat.Berkeley.EDU] 
Sent: woensdag 28 januari 2009 6:38
To: Vinuela, Ana
Cc: bioconductor at stat.math.ethz.ch
Subject: Re: [BioC] Error in BioMart and wormbase

Dear Ana,

It looks like there is a problem with the XML configuration file for
that dataset.  If you upgrade to using the dev version of biomaRt
(http://bioconductor.org/packages/2.4/bioc/html/biomaRt.html) you should
be fine for this dataset, as that version does not depend on this XML
file anymore.

worbase_gene works for me see below:

> library(biomaRt)
>
> wormbase = useMart("wormbase_current", dataset = "wormbase_gene")

Checking attributes ... ok
Checking filters ... ok
>
> att = listAttributes(wormbase)
> att[1:10,]
                name                          description
1            species                              Species
2               gene                           Gene WB ID
3      sequence_name                 Sequence Name (Gene)
4        public_name                     Gene Public Name
5                cds                  Sequence Name (CDS)
6           cgc_name                        Gene CGC Name
7         transcript           Sequence Name (Transcript)
8        name_dmlist                  Gene Names (merged)
9         cds_dmlist        Sequence Names (CDS) (merged)
10 transcript_dmlist Sequence Names (Transcript) (merged)

> sessionInfo()
\R version 2.8.0 (2008-10-20)
powerpc-apple-darwin8.11.1

locale:
C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] biomaRt_1.99.4

loaded via a namespace (and not attached):
[1] RCurl_0.92-0 XML_1.98-1



>
> Dear all,
>
> I've been experience a problem with BioMart when I tried to access 
> wormbase. I am getting an error when I tried to use a specific dataset

> (wormbase_gene). This problem do not exist when I access any other 
> dataset from wormbase. Besides, few months ago a used this code 
> without problems.
>
>
>> library(biomaRt)
>> wormbase = useMart("wormbase_current", dataset = "wormbase_gene")
> Checking attributes and filters ...Error in if (xmlGetAttr(xml,
> "displayType") == "list" && type != "boolean") options =
> parseOptions(xml) :
>   missing value where TRUE/FALSE needed
>
>> listDatasets(wormbase)
>                 dataset        description version
> 1        wormbase_paper              Paper
> 2         wormbase_gene               Gene
> 3 wormbase_anatomy_term       Anatomy Term
> 4 wormbase_expr_pattern Expression Pattern
> 5      wormbase_go_term            GO Term
> 6         wormbase_rnai               RNAi
> 7    wormbase_phenotype          Phenotype
> 8    wormbase_variation          Variation
>
>> wormbase = useMart("wormbase_current", dataset = "wormbase_paper")
> Checking attributes and filters ... Ok
>
>
>
> I will appreciate any help.
>
> Ana.
>
>
> ##############################
>> sessionInfo()
> R version 2.8.0 (2008-10-20)
> i386-pc-mingw32
>
> locale:
> LC_COLLATE=Dutch_Netherlands.1252;LC_CTYPE=Dutch_Netherlands.1252;LC_M
> ON
> ETARY=Dutch_Netherlands.1252;LC_NUMERIC=C;LC_TIME=Dutch_Netherlands.12
> 52
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
>
> other attached packages:
> [1] biomaRt_1.16.0
>
> loaded via a namespace (and not attached):
> [1] RCurl_0.91-0 XML_1.94-0.1
>
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