On Thu, Aug 2, 2012 at 9:58 AM, John Coulthard wrote: > > Hi > > When following the instructions in the biomaRt.pdf I get the > error below which ends 'Please report this to the mailing list'. > > Did I do something wrong or do I wait for something to be fixed? > I am behind a proxy server but I can download packages so I don't think > that is the issue. > > Many thanks > John > > > $ R > > R version 2.15.1 (2012-06-22) -- "Roasted Marshmallows" > Copyright (C) 2012 The R Foundation for Statistical Computing > ISBN 3-900051-07-0 > Platform: x86_64-unknown-linux-gnu (64-bit) > > R is free software and comes with ABSOLUTELY NO WARRANTY. > You are welcome to redistribute it under certain conditions. > Type 'license()' or 'licence()' for distribution details. > > Natural language support but running in an English locale > > R is a collaborative project with many contributors. > Type 'contributors()' for more information and > 'citation()' on how to cite R or R packages in publications. > > Type 'demo()' for some demos, 'help()' for on-line help, or > 'help.start()' for an HTML browser interface to help. > Type 'q()' to quit R. > > > library(biomaRt) > > ensembl = useMart("ensembl", dataset = "hsapiens_gene_ensembl") > > affyids = c("202763_at", "209310_s_at", "207500_at") > > > getBM(attributes = c("affy_hg_u133_plus_2", "entrezgene"), filters = > "affy_hg_u133_plus_2",values = affyids, mart = ensembl) > > > & > nbsp; V1 > 1 > http://www.w3.org/TR/html4/loose.dtd> > 2 > CONTENT=text/html; charset=iso-8859-1> > 3 > > & > nbsp; ERROR: The > requested URL could not be retrieved > Hi, John. I note below in sessionInfo() that you are using an outdated version of biomaRt. You might want to update by doing: biocLite('biomaRt') Using the current release version (2.12.0), I was not able to reproduce your problem. That said, it looks like biomaRt cannot connect to biomart. Does listMarts(ensembl) work for you? This could be a temporary problem or it could be that you are behind a firewall and need to set up a proxy for R to connect to the internet. Sean > 4 > > 5 > > & > nbsp; > 6 >

ERROR

> Error in getBM(attributes = c("affy_hg_u133_plus_2", "entrezgene"), > filters = "affy_hg_u133_plus_2", : > > 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. > > > > That html reads.... > ERROR > The requested URL could not be retrieved > > While trying to process the request: > > > POST /biomart/martservice? HTTP/1.1 > > Host: www.biomart.org > > Accept: */* > > Proxy-Connection: Keep-Alive > > Content-Length: 483 > > Expect: 100-continue > Content-Type: > multipart/form-data; boundary=----------------------------2224e5531f52 > > > The following error was encountered: > > Invalid Request > > Some aspect of the HTTP Request is invalid. Possible problems: > > Missing or unknown request method > Missing URL > Missing HTTP Identifier (HTTP/1.0) > Request is too large > Content-Length missing for POST or PUT requests > Illegal character in hostname; underscores are not allowed > > Your cache administrator is cacheadmin@udcf.gla.ac.uk. > Generated Thu, 02 Aug 2012 11:12:23 GMT by south (squid/2.7.STABLE9) > > > > sessionInfo() > R version 2.15.1 (2012-06-22) > Platform: x86_64-unknown-linux-gnu (64-bit) > > locale: > [1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C > [3] LC_TIME=en_GB.UTF-8 LC_COLLATE=en_GB.UTF-8 > [5] LC_MONETARY=en_GB.UTF-8 LC_MESSAGES=en_GB.UTF-8 > [7] LC_PAPER=C LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] biomaRt_2.10.0 > > loaded via a namespace (and not attached): > [1] AnnotationDbi_1.16.19 Biobase_2.14.0 Biostrings_2.22.0 > [4] BSgenome_1.22.0 DBI_0.2-5 GenomicFeatures_1.6.9 > [7] GenomicRanges_1.6.7 IRanges_1.12.6 RCurl_1.91-1 > [10] RSQLite_0.11.1 rtracklayer_1.14.4 tools_2.15.1 > [13] XML_3.9-4 zlibbioc_1.0.1 > > > > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]