[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 âBiocInstallerâ 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 âlimmaâ
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 âlimmaâ successfully unpacked and MD5 sums checked
package âedgeRâ 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 âreadDGEâ in specified packages and libraries:
you could try â??readDGEâ
> ?read.delim
starting httpd help server ... done
> ?DGEList
No documentation for âDGEListâ in specified packages and libraries:
you could try â??DGEListâ
> d <- readDGE("targets")
Error: could not find function "readDGE"
> ?exact
No documentation for âexactâ in specified packages and libraries:
you could try â??exactâ
> ?exactTest
No documentation for âexactTestâ in specified packages and libraries:
you could try â??exactTestâ
> y <- DGEList(counts = 5)
Error: could not find function "DGEList"
> ?DGEList
No documentation for âDGEListâ in specified packages and libraries:
you could try â??DGEListâ
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