Statomics, software for statistical analysis, especially for testing multiple hypotheses related to genomic and proteomic data. Version 0.4 (beta).

Copyright (C) 2001-2005 by David R. Bickel.

The contents of these files are subject to the Mozilla Public License Version 1.1 (the "License"); you may not use these files except in compliance with the License. You may obtain a copy of the License at http://www.mozilla.org/MPL/

Software distributed under the License is distributed on an "AS IS" basis, WITHOUT WARRANTY OF ANY KIND, either express or implied. See the License for the specific language governing rights and limitations under the License.

 

Instructions for running a tutorial

  1. Download R (www.r-project.org).
  2. Install and learn how to use R.
  3. If you wish to plot networks or other graphs, install a Postscript viewer or PS-to-PDF converter, and install GraphViz after downloading it (www.graphviz.org). You need not learn GraphViz syntax, as Statomics should automatically interface with dot via the hard disk and calls to the operating system. [This step was slightly modified on 2/9/05.]
  4. Place the Statomics files that end with '.r' or '.jar' in the same directory.
  5. Launch R, then set the working directory to the directory with those Statomics files.
  6. Type the R commands shown in one of the following Statomics tutorial files ending in '.rtf':
    • For calculations related to the detection or estimation of degrees of differential gene expression, run the commands in the degrees tutorial file, reading the comments to understand how the software implements the paper referenced at the top of that file.
    • For calculations related to confidence intervals of the false discovery rate, run the commands in the confidence-interval tutorial file, reading the comments to understand how the software implements the paper referenced at the top of that file.
    • For calculations related to the reconstruction of networks, install this Java software* and run the commands in the network tutorial file, reading the comments to understand how the software implements the paper referenced at the top of that file. Warning to PC users: some features of the network reconstruction software might not work on Windows platforms without source code modification (warning added 5/17/04).
* Mac OS X comes with the Java software pre-installed