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
2
3
&
nbsp; ERROR: The requested URL could not be retrieved
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]]