Hi, I just updated biomaRt to the latest version and I'm experiencing some
problems. Basically, getLDS shows the output in the screen but does not save
it.

For instance, executing the code that comes as an example in the
documentation and trying to save the output in mymap.

>     human = useMart("ensembl", dataset = "hsapiens_gene_ensembl")
Checking attributes ... ok
Checking filters ... ok
>      mouse = useMart("ensembl", dataset = "mmusculus_gene_ensembl")
Checking attributes ... ok
Checking filters ... ok
> mymap <- getLDS(attributes = c("hgnc_symbol","chromosome_name",
"start_position"), filters = "hgnc_symbol", values = "TP53", mart = human,
attributesL = c("chromosome_name","start_position"), martL = mouse)
TP53    17    7512445    11    69393861
> mymap
                                                         V1
1                                           HTTP/1.1 200 OK
2                       Date: Fri, 05 Jun 2009 08:21:10 GMT
3 Server: Apache/2.2.9 (Debian) mod_perl/2.0.4 Perl/v5.10.0
4                                         Connection: close
5                                Transfer-Encoding: chunked
6                                  Content-Type: text/plain

When calling getLDS the screen shows the desired map, but what gets actually
saved is this HTTP info. The same happens when doing genome-wide queries
instead of only based on TP53. Help please?

Thank you,

David

-- 
David Rossell, PhD
Manager, Bioinformatics and Biostatistics unit
IRB Barcelona
Tel (+34) 93 402 0217
Fax (+34) 93 402 0257
http://www.irbbarcelona.org/bioinformatics

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