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DEDS (Differential Expression via Distance Summary)

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

  1. Download the file DEDS.zip and save it on your desktop.
  2. Start the R program by double clicking on the Rgui.exe icon.
  3. Click on the menu Packages and select "Install package from local zip file...".
  4. 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]