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 use of STAC Station, an application for performing STAC analysis and for viewing the results of STAC analysis. See also the STAC 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 technical manual.

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 higher installed on your system. You can get Java from SUN at http://java.sun.com/j2se/1.4.2/download.html

STAC Input

NOTE: STAC analyzes data in the form of binary aberration calls. So gains and losses are analyzed separately and separate input files must be prepared for each case.
 
NOTE: For best results STAC analysis should be run on only a single chromosome arm at a time, omitting centromeres and other regions of poor coverage.
 
Currently STAC takes as input data in two possible formats.
  1. Location data:
  2. Span data:
Examples that you can run through STAC are given with the STAC 1.1 distribution in the subdirectory "Examples".

Go here for more notes on formatting and pre-processing

Usage

You open a file, or directory of files, to analyze (which must be in one of the two input formats given above. Once a file has been been analyzed, the STAC results can be re-opened just 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 has two File  Open 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.

Note: STAC Station can open one file at a time to analyze, or a directory of files. Once a file or directory is open to analyze, the "ANALYZE" button becomes enabled.

STAC can also view multiple 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). The file opened to analyze does not appear in the results viewer until "ANALYZE" has been pressed and the analysis is complete.

As you perform analyses on files, they get added to the viewer list. Similarly as you open results files to view, they also get added to the list. You can then 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.

Analysis Options

There are two options you can set regarding how the analysis is performed. These are "number of permutations" and "search parameter". If your file is "span formatted" (see above), then there is a third option called the "resolution".

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.