[BioC] edgeR usage

narges [guest] guest at bioconductor.org
Wed Apr 11 18:38:54 CEST 2012


Hi, I am new to the edgeR field and I do not know why it does not work.
I have installed the R (latest version 2.15.0)and according to what is mentioned in bioconductor web site I use these two commands:
source("http://bioconductor.org/biocLite.R")
biocLite("edgeR")
the messages show everything is installed successfully but when I type for example:
d <- readDGE (targets)
the error is:
Error: could not find function "readDGE"
Does it mean the edgeR is not successfully installed?
what should I do?

 -- output of sessionInfo(): 

> source("http://bioconductor.org/biocLite.R")
Warning in install.packages("BiocInstaller", repos = a["BioCsoft", "URL"]) :
  'lib = "C:/Program Files/R/R-2.15.0/library"' is not writable
trying URL 'http://www.bioconductor.org/packages/2.10/bioc/bin/windows/contrib/2.15/BiocInstaller_1.4.3.zip'
Content type 'application/zip' length 41610 bytes (40 Kb)
opened URL
downloaded 40 Kb

package ‘BiocInstaller’ successfully unpacked and MD5 sums checked

The downloaded binary packages are in
        C:\Users\narges\AppData\Local\Temp\RtmpEzB8mw\downloaded_packages
BiocInstaller version 1.4.3, ?biocLite for help
> 
> biocLite("edgeR")
BioC_mirror: http://bioconductor.org
Using R version 2.15, BiocInstaller version 1.4.3.
Installing package(s) 'edgeR'
also installing the dependency ‘limma’

trying URL 'http://www.bioconductor.org/packages/2.10/bioc/bin/windows/contrib/2.15/limma_3.12.0.zip'
Content type 'application/zip' length 1533961 bytes (1.5 Mb)
opened URL
downloaded 1.5 Mb

trying URL 'http://www.bioconductor.org/packages/2.10/bioc/bin/windows/contrib/2.15/edgeR_2.6.0.zip'
Content type 'application/zip' length 1563602 bytes (1.5 Mb)
opened URL
downloaded 1.5 Mb

package ‘limma’ successfully unpacked and MD5 sums checked
package ‘edgeR’ successfully unpacked and MD5 sums checked

The downloaded binary packages are in
        C:\Users\narges\AppData\Local\Temp\RtmpEzB8mw\downloaded_packages
> ?readDGE
No documentation for ‘readDGE’ in specified packages and libraries:
you could try ‘??readDGE’
> ?read.delim
starting httpd help server ... done
> ?DGEList
No documentation for ‘DGEList’ in specified packages and libraries:
you could try ‘??DGEList’
> d <- readDGE("targets")
Error: could not find function "readDGE"
> ?exact
No documentation for ‘exact’ in specified packages and libraries:
you could try ‘??exact’
> ?exactTest
No documentation for ‘exactTest’ in specified packages and libraries:
you could try ‘??exactTest’
> y <- DGEList(counts = 5)
Error: could not find function "DGEList"
> ?DGEList
No documentation for ‘DGEList’ in specified packages and libraries:
you could try ‘??DGEList’

--
Sent via the guest posting facility at bioconductor.org.



More information about the Bioconductor mailing list