Statomics
Statomics is a software suite for the statistical analysis of genomic and proteomic data. Statomics was derived from BioinfoStat and PLATO. The software can be used for many other areas of application, but most of it was designed for gene expression microarrays. Statomics implements methods that address problems with testing multiple hypotheses, especially the methods described in the papers listed at the beginnings the tutorial files included with the software; the full text of each paper may be downloaded.
Statomics is compatible with Windows, UNIX, Linux, and Macintosh operating systems. It requires a recent installation of R. The related package HighProbability runs on S-PLUS as well as R.
The source code of the Statomics software for multiple comparisons may be downloaded as a zip archive file.
Statomics Version 0.2, Version 0.3, Version 0.4, and the current version (0.4 with improved documentation and compression) were first made available from this web site as free open source software on 1/31/04, 3/29/04, 2/9/05, and 10/21/06, respectively. (Version 0.4 is exactly the same as Version 0.3, except for minor modifications of two documentation files and a bug fix for network reconstruction: the function optimal.y.lag now takes the absolute value of the correlation coefficient before finding the maximum. Thus, the algorithm described in the associated 2005 Bioinformatics paper is closer to that of Version 0.4, but, due to misplaced reliance on the algorithm of Version 0.3, the preprint and online advance versions of the paper report an underestimate of the "probability that a time ordering observed for two associated genes is misleading." The online supplementary figures were corrected accordingly on 3/3/05, and the corresponding corrected article is scheduled to appear in print on 4/15/05. Since the demo documentation RTF file was created using Version 0.3, its p-values are substantially lower than those obtained using Version 0.4.) The file extension of the archives was changed to .tar.gz for compatability with Windows on 5/17/04, and two references to papers were corrected on 5/18/04. The current version consists of files with these names: MultTests.r; FDRCI.r; README.htm; General.r; Corromics.jar; TUTORIAL_CI; Corromics.java; BiobaseSupp.r; TestStats.r; GraphVizSupp.r; LICENSE.htm; Proteomics.r; TUTORIAL_net.rtf; TUTORIAL1.rtf; Estimation.r; MultCorr.r.
