[BioC] Problem with getBM function in biomaRt package
James W. MacDonald
jmacdon at med.umich.edu
Tue Jul 4 20:43:02 CEST 2006
Luo Weijun wrote:
> Hello all,
> I am trying to get gene symbols and full gene names
> (description) for a long list of (>=8000) genes. I use
> getBM function in biomaRt package. And the code is
> pretty much the same as Jim¡¯s ¡®HowTo: get pretty
> HTML output for my gene list¡¯ vignette. Everything
> works fine when I use a much shorter list (100 genes),
> i.e. igenes= hs95av2Entrezg7[1:100] in the following
> codes. But when igene= hs95av2Entrezg7 (full gene
> list), getBM doesn¡¯t work, and returns an error
> Loading required package: XML
> Loading required package: RCurl
>>mart <- useMart("ensembl", "hsapiens_gene_ensembl")
> Checking attributes and filters ... ok
> <escription"), filter = "entrezgene",values = igenes,
> mart = mart, output = "list",na.value ='')
> ##(note here my orginal input is:
> genelist=getBM(attributes =
> c("hgnc_symbol","description"), filter =
> "entrezgene",values = igenes, mart = mart, output =
> "list",na.value ='')
> ##and this long line is truncated in the terminal
> screen somehow)
> Error in postForm(paste(mart at host, "?", sep = ""),
> query = xmlQuery) :
> couldn't connect to host
> Since Jim also suggests that RMySQL is much faster
> than RCurl, I also tried to install RMySQL package,
> but the error messages says there is no such package,
> even though I did see RMySQL is there in the
> contributed package list in all mirror sites of CRAN I
> tried. Not sure what is the problem.
>>install.packages('RMySQL', repos =
> Warning in download.packages(pkgs, destdir = tmpd,
> available = available, :
> no package 'RMySQL' at the repositories
Running getBioC version 0.1.6 with R version 2.3.0
Running biocinstall version 1.8.4 with R version 2.3.0
Your version of R requires version 1.8 of Bioconductor.
also installing the dependency 'DBI'
trying URL 'http://cran.fhcrc.org/bin/windows/contrib/2.3/DBI_0.1-10.zip'
Content type 'application/zip' length 348086 bytes
Content type 'application/zip' length 899757 bytes
package 'DBI' successfully unpacked and MD5 sums checked
package 'RMySQL' successfully unpacked and MD5 sums checked
The downloaded packages are in
C:\Documents and Settings\dd1\Local
updating HTML package descriptions
I assume there is also a MacOS binary on BioC as well, but don't know
for sure. If not, you might look into installing the tools required to
> Here is my session info
> Version 2.3.1 (2006-06-01)
> attached base packages:
>  "methods" "stats" "graphics" "grDevices"
> "utils" "datasets"
>  "base"
> other attached packages:
> biomaRt RCurl XML
> "1.6.0" "0.6-2" "0.99-7"
> I actually can¡¯t even do sessionInfo after the getBM
> line got broken.
> Error in gzfile(file, "rb") : unable to open
> In addition: Warning messages:
> 1: list.files:
> '/Library/Frameworks/R.framework/Resources/library' is
> not a readable directory
> 2: cannot open compressed file
> Thank you so much for your kind help!
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James W. MacDonald
University of Michigan
Affymetrix and cDNA Microarray Core
1500 E Medical Center Drive
Ann Arbor MI 48109
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