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)
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 <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
</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 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.
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