I deciphered the column of html I was getting returned by getBM, it says...
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 [email protected].
Generated Thu, 02 Aug 2012 11:12:23 GMT by south (squid/2.7.STABLE9)
From: [email protected]
To: [email protected]
Date: Thu, 2 Aug 2012 10:48:17 +0000
Subject: [BioMart Users] R biomaRt 'Please report this to the mailing list'
Hi
When following the instructions in the biomaRt.pdf I get the error below which
ends 'Please report this to the mailing list' (I hope it means the biomart
mailing list rather than R or bioconductor lists).
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 2.14.1 (2011-12-22)
Copyright (C) 2011 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
Platform: x86_64-pc-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 <!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
&
nbsp; <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
&
nbsp; </HEAD><BODY>
6
<H1>ERROR</H1>
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.
> sessionInfo()
R version 2.14.1 (2011-12-22)
Platform: x86_64-pc-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 &nb
s
p; 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] RCurl_1.91-1 XML_3.9-4
>
> source("http://bioconductor.org/biocLite.R";)
BiocInstaller version 1.2.1, ?biocLite for help
> biocLite("org.Hs.eg.db")
BioC_mirror: 'http://www.bioconductor.org'
Using R version 2.14, BiocInstaller version 1.2.1.
Installing package(s) 'org.Hs.eg.db'
Installing package(s) into \u2018/usr/local/lib/R/site-library\u2019
(as \u2018lib\u2019 is unspecified)
Warning
in install.packages(pkgs = pkgs, repos = repos, ...) :
'lib = "/usr/local/lib/R/site-library"' is not writable
Would you like to create a personal library
~/R/x86_64-pc-linux-gnu-library/2.14
to install packages into? (y/n) y
trying URL
'http://www.bioconductor.org/packages/2.9/data/annotation/src/contrib/org.Hs.eg.db_2.6.4.tar.gz'
Content type 'application/x-gzip' length 46530609 bytes (44.4 Mb)
opened URL
==================================================
downloaded 44.4 Mb
* installing *source* package \u2018org.Hs.eg.db\u2019 ...
** R
** inst
etc, etc.
_______________________________________________
Users mailing list
[email protected]
https://lists.biomart.org/mailman/listinfo/users
_______________________________________________
Users mailing list
[email protected]
https://lists.biomart.org/mailman/listinfo/users
