This function contains functions that calculate various statistics of differential expression for microarray data,
including t statistics, fold change, F statistics, SAM, moderated t and F statistics and B statistics. It also
implements a new methodology called DEDS (Differential Expression via Distance Summary), which selects differentially expressed genes by integrating and summarizing a set of statistics using a weighted distance approach.Version (Date): 1.0.2 (8.05.04)
Author: Yuan Yuan Xiao
Installation
Option A) Automatic
Start R on your computer. At the R prompt, type
install.packages("DEDS",contriburl="http://www.biostat.ucsf.edu/jean/software")
To install the package on a specific directory (e.g. "mydir")
install.packages("DEDS",contriburl="http://www.biostat.ucsf.edu/jean/software",lib="mydir")
Option B) Manual
- Download the file DEDS.zip and save it on your desktop.
- Start the R program by double clicking on the Rgui.exe icon.
- Click on the menu Packages and select "Install package from local zip file...".
- Select the file DEDS.zip to install the package.
To load the library
Type at the R prompt.
library(DEDS)
To update the package type:
update.packages(contriburl="http://www.biostat.ucsf.edu/jean/software")
Reference
Y. H. Yang*, Y. Y. Xiao* and M. Segal (2004). Identifying differentially expressed genes from microarray experiments via statistic synthesis. Bioinformatics (accepted) [pdf]