- How microarray chips work (from an educational site curated by the Office of Science Education at NIH).
3rd Party Microarray Analysis Tools
- GeneSifter: Web-based system for the analysis of gene expression data. Some screenshots here. Educational material and user guide available at http://www.genesifter.net/web/training.html.
- TIGR MultiExperiment Viewer (TMev): an open source Java application for analyzing gene expression data developed by TIGR (The Institute for Genomic Research). Their web site contains pointers to a user manual and to training slides.
- BRB ArrayTools: integrated package for the visualization and statistical analysis of DNA microarray gene expression data. Developed by Richard Simon at NCI, Biometric Research Branch (BRB). According to the description on the site, the software "was developed by professional statisticians experienced in the analysis of microarray data and involved in the development of improved methods for the design and analysis of microarray based experiments". It does not have a separate GUI, rather appears as an add-in in Excel. Richard Friedman recommends this, it is one of the programs that he is using in his consulting engagements.
- ARDAS Version 2: 3rd Millenium produces this microarray repository and data analysis system. It can handle both Affymetrix and two-color experiments. The repository is based on Oracle. There is also a LIMS component which only handles two-color array experiments. The Analysis module supports aspects of R, Bioconductor and LIMMA, and the MAS5, RMA and d-Chip methods. It is a server-based system with a web interface.
- GEPAS: The Gene Expression Pattern Analysis Suite (GEPAS) is an integrated web-based pipeline for the analysis of gene expression patterns. GEPAS includes tools for normalization, clustering, differential gene expression, predictors, array CGH and functional annotation. Their web site contains several good tutorials.
- Ocimumbio: An Indian software and biotech services company that makes a geWorkbench-like application for microarray analysis. See Genowiz for the software and data_analysis for analysis details.
- Affymetrix Array Analysis from NCI - a page with background material on affymetrix array analysis.
- FiRe Find Regulons - in NZZ newspaper.
- Y-Bio v1.1 - Y-Bio v1.1, Foundation for Penguin ClusterWare Life Sciences Suite
- array2bio - another nice reference to how a commercial outfit analyzes microarray data.
- Bernd rates the Partek GS program great! Somewhere on Affymetrix.com. "Regulation Analysis of ChIP-on-Chip Studies Using Partek* GS and Affymetrix* Human Promoter TilingArrays
- Collection of links - One individual's large collection of links to microarray analysis packages.