[BioC] edgeR usage

[James W. MacDonald]

You need to load a package into R before you can use it.

library(edgeR)
?readDGE

Best,

Jim



On 4/11/2012 12:38 PM, narges [guest] wrote:
> 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.
>
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-- 
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099