[main page] [software] [protocols]

Current Versions:

  • GalFileMaker: 1.2.0
  • ArrayMaker : 2.3.2
  • ScanAlyze : 2.44
  • AMAD : 1.01
  • Cluster : 2.10
  • TreeView : 1.45


  • AMAD submit script update

Making Arrays

ArrayMaker Version 2 is now available!
Click here for the ArrayMaker HomePage.

Image Analysis

ScanAlyze: Process fluorescent images of microarrays. Includes semi-automatic definition of grids and complex pixel and spot analyses. Outputs to tab-delimited text files for transfer to any database. Manual available. For Windows95/98/NT only.


Coming Soon: NOMAD

AMAD: Another Microarray Database. (Jan 1, 2000 - version 1.01)
This is a simple yet very effective flat file database designed specifically for microarray data. It will run on any web server that supports PERL.

Data Analysis

Gal File Maker v1.2 This program serves two functions: Conversion of a file of 96 well plates into a file of 384 well plates, and conversion of a file of 384 well plates into an Axon GenePix Gene Array List file (.gal file). Several options are available for this latter function, including spot size, spacing, and orientation of plate in the arrayer with respect to the slides.Here is a screenshot

Cluster: Perform a variety of types of cluster analysis and other types of processing on large microarray datasets. Currently includes hierarchical clustering and self-organizing maps (SOMs). Hierarchical clustering methods described in Eisen et al. (1998) PNAS 95:14863. Designed for use with TreeView. Cluster/TreeView manual available. For Windows95/98/NT only.

TreeView: Graphically browse results of clustering and other analyses from Cluster. Supports tree-based and image based browsing of hierarchical trees. Multiple output formats for generation of images for publications. Cluster/TreeView manual available. For Windows95/98/NT only.

J-Express: A Java implementation of hierachical clustering, self organized maps, and principal component analysis, with several different viewing options and output formats. Requires Java Runtime Environment 1.2 or higher