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 [[alternative HTML version deleted]]

Nevermind, the problem was due to RCurl and goes away with the latest version (0.98-0). I had to install it from source as it is not yet available in the CRAN repository (update.packages won't update it to the latest version). Sorry for the false alarm, David On Fri, Jun 5, 2009 at 10:26 AM, David Rossell < david.rossell@irbbarcelona.org> wrote: > 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 > -- 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 [[alternative HTML version deleted]]