R Packages

1. From CRAN

Install these packages from CRAN. Always check the "install dependencies" box.

• DPpackage
• ggplot2
• gsubfn
• hexbin
• languageR
• lme4
• MCMCglmm
• multcomp
• plyr
• reshape

A quicker way to do it is to copy and paste the following line at your R prompt:

install.packages(c("DPackage", "ggplot2", "gsubfn","hexbin","languageR","lme4","MCMCglmm","multcomp","plyr","reshape"))

2. From Bioconductor

When you install those packages you will get this warning: Warning: dependencies ‘marray’, ‘affy’, ‘Biobase’, ‘Rgraphviz’, ‘’ are not available. To fix it, install the standard packages from [http://www.bioconductor.org/docs/install/ Bioconductor] by doing the following at the R prompt:

source("http://bioconductor.org/biocLite.R")
biocLite(lib='/Library/Frameworks/R.framework/Resources/library/')

adjusting lib as appropriate for your OS. The example above is for Mac OS X. For Windows use:

biocLite(lib='C:\\Program Files\\R\\R-2.11.1\\library')

adjusting the version number as appropriate. (n.b. You must have Administrator privileges to install anything under C:/Program Files/)