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.

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/windo ws/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/windo ws/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/windo ws/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. > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- James W. MacDonald, M.S. Biostatistician University of Washington Environmental and Occupational Health Sciences 4225 Roosevelt Way NE, # 100 Seattle WA 98105-6099