STAC Station User's Guide

STAC

STAC (Significance Testing for Aberrant Copy-Number) tests for significantly concordant aberration across multiple samples in array CGH data.

This document describes the general usage of STAC Station v1.2, an application for performing STAC analysis and for viewing the results of STAC analysis. For a more detailed description see also the STAC Station tutorial.

STAC analysis requires aberration data for each of a number of different samples and it performs a statistical test to determine locations which are concordantly aberrant across individuals more than should be expected by chance. The statistical theory and algorithm are desribed in the STAC publication. The algorithm described in that paper is implemented exactly in version 1.1. The algorithm has been modified slightly to run much faster without affecting the results and this is implemented in version 1.2 (The details of this modification will be given in a technical document by Aug 20th, please check back.)

Reference

If you use STAC in your research, please reference the following publication:

Diskin SJ, Eck T, Greshock J, Mosse YP, Naylor T, Stoeckert CJ Jr., Weber BL, Maris JM and Grant GR. (2006) STAC: A method for testing the significance of DNA copy-number aberrations across multiple array-CGH experiments. Genome Research (in press).

Installation

First make sure you have Java 1.4 or above installed on your system. You can get Java from SUN at http://java.sun.com/j2se/1.4.2/download.html

STAC Input

STAC analyzes data in the form of binary aberration calls. So gains and losses (or any other type of aberration) are analyzed separately and separate input files must be prepared for each case.
 
IMPORTANT: For results local to a chromosome arm, STAC analysis should be run on only a single chromosome arm at a time, omitting centromeres and other regions of poor coverage.
 
Currently STAC Station takes input data in two possible formats.
  1. Location data:
  2. Span data:
NOTE: The full set of input files used in Diskin et al (2006) are provided with the STAC Station 1.2 distribution in the subdirectory called "Examples".

Go here for more notes on formatting and pre-processing

Usage: STAC Analysis

You open either a single file or directory of files to analyze. Once a file has been been analyzed, the STAC results can be re-opened to review the results, without re-analyzing - because analyzing can take a considerable amount of time. If the file with the STAC input is called "stacinput.txt" then the results will be saved as stacinput.txt.stac. This is why the file menu File  Open has two options:
  1. "Open to Run" which takes a STAC input file to be analyzed, as described above.
  2. "Open to View" which takes a STAC analysis results file and opens it just to view.

STAC Station can open one file at a time to analyze, or a directory of files. If you open a single file, the ANALYZE button will become enabled; press ANALYZE to perform STAC analysis on the current file. If you open a directory, the analysis will start automatically for each of the appropriately formatted STAC input file in that directory.

STAC Station can also view multiple results files (the number of files you can open is limited only by memory - if you run out of memory change the "256" in the command used to execute STAC Station to something higher).

NOTE: As you open files for viewing or analyses, they get added to the viewer list. You may scroll through the files to view the data. Once the analysis for a file is complete, you can also browse through the results files using the forward and back arrow buttons. The current file number and the total number of files is shown in the status bar at the bottom of the window along with the state of key results display options.

Analysis Options

There are two options you can set regarding how the analysis is performed. These are "number of permutations" and "resolution". This second option is only meaningful if your data is "span formatted" (see above).

Note: The "search parameter" option present in STAC 1.1 has been deprecated due to the optimized search strategy available in STAC 1.2.

Display Options

There are many display options.

Output

These options are on the File  Save menu.

General Operating Characteristics

There are several factors that can influence the sensitivity of STAC and the time required for execution. We summarize each of these here.