R and BioConductor install

R and BioConductor install
How to download and install R and bioconductor

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1. Downloading and unpacking R from www.r-project.org

Go to www.r-project.org and download the newest R source package

Newest direct link:

http://mirrors.sunsite.dk/cran/src/base/R-1.8.1.tgz

Lates version on sunsite:

http://mirrors.sunsite.dk/cran/src/base/R-latest.tgz

or in shell:

wget http://mirrors.sunsite.dk/cran/src/base/R-latest.tgz

Save somewhere and unpack with the file with:

tar -zxvf R-latest.tgz

2. Installing R as a user

cd RDIR
./configure --prefix=/home/serine/R
make
make install

You now have R installed in /home/serine/R/bin, to start THIS VERSION OF R - call

/home/serine/R/bin/R

3. Installing Bioconductor and other packages

In R:

source("http://www.bioconductor.org/biocLite.R")
biocLite()
biocLite(c("limma", "genefilter","siggenes"))
install.packages("qvalue")
install.packages("GeneTS")
install.packages("epitools")
install.packages("combinat")
#The genetics package and dependents
install.packages("gdata")
install.packages("MASS")
install.packages("mvtnorm")
install.packages("genetics")
update.packages()

4. Using R and Bioconductor

From a directory with cellfiles:

/home/serine/R/bin/R

In the R console:

library(affy)
Data<-ReadAffy()
eset<-rma(Data)
write.exprs(eset, file="mydata.txt")

Quick copy and paste after downloading

tar -zxvf RFILE.tgz
cd RDIR
./configure --prefix=R_INSTALL_DIR
make
make install
R_INSTALL_DIR/bin/R
source("http://www.bioconductor.org/biocLite.R")
biocLite()
biocLite(c("limma", "genefilter","siggenes"))
install.packages("qvalue")
install.packages("GeneTS")
update.packages()