[BioC] Problem with getBM function in biomaRt package

[James W. MacDonald]

Hi Weijun,

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
> message. 
> 
> 
>>library(biomaRt)
> 
> Loading required package: XML
> Loading required package: RCurl
> 
>>mart <- useMart("ensembl", "hsapiens_gene_ensembl")
> 
> Checking attributes and filters ... ok
> 
> load('/Users/luow/project/microarraydata/annotation/hs95av2Entrezg7.Rdata')
> 
>>igenes=hs95av2Entrezg7
> 
> <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 =
> 
> "http://www.biometrics.mtu.edu/CRAN/")      
> Warning in download.packages(pkgs, destdir = tmpd,
> available = available,  : 
>          no package 'RMySQL' at the repositories

 > source("http://www.bioconductor.org/biocLite.R")
 > biocLite("RMySQL")
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
opened URL
downloaded 339Kb

trying URL 
'http://bioconductor.org/packages/1.8/omegahat/bin/windows/contrib/2.3/RMySQL_0.5-6.zip'
Content type 'application/zip' length 899757 bytes
opened URL
downloaded 878Kb

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 
Settings\Temp\Rtmp0c07pb\downloaded_packages
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 
build packages.

http://cran.fhcrc.org/bin/macosx/RMacOSX-FAQ.html#How-to-install-packages

HTH,

Jim


> 
> 
> Here is my session info 
> 
>>sessionInfo()
> 
> Version 2.3.1 (2006-06-01) 
> powerpc-apple-darwin8.6.0 
> 
> attached base packages:
> [1] "methods"   "stats"     "graphics"  "grDevices"
> "utils"     "datasets" 
> [7] "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.
> 
>>sessionInfo()
> 
> Error in gzfile(file, "rb") : unable to open
> connection
> In addition: Warning messages:
> 1: list.files:
> '/Library/Frameworks/R.framework/Resources/library' is
> not a readable directory 
> 2: cannot open compressed file
> '/Library/Frameworks/R.framework/Resources/library/biomaRt/Meta/package.rds'
> 
> 
> 
> Thank you so much for your kind help!
> Weijun
> 
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor


-- 
James W. MacDonald
University of Michigan
Affymetrix and cDNA Microarray Core
1500 E Medical Center Drive
Ann Arbor MI 48109
734-647-5623



**********************************************************
Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues.