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• Microarray troubleshooting: image gallery
• Microarray troubleshooting guide from Genisphere
• Technical Aspects of Microarray Production
• A Concise Guide to cDNA Microarray Analysis – II
• The-Science-Lab.com - directory of Biology related websites

Software for microarray analysis and databases:

• Dapple from Washington University in St. Louis. (UNIX/Linux/Mac OSX)
• F-scan from NIH (UNIX/Linux, Windows, Mac)
• ScanAlyze from Michael Eisen's lab (Windows)
• Spotfinder from TIGR (Windows)
• UCSF Spot from Jain Lab at UCSF (Windows)

• GenePix Pro from Axon Instruments (Windows)
• ImaGene from BioDiscovery (Windows)
• ArrayPro from MediaCybernetics (Windows)
• ArrayVision from Imaging Research, Inc (Windows)

• GPAP from OSU Microarray Core and Bioinformatics Resource Facilities (Web)
• Bioconductor and R-project statistical environment
• ANOVA from Churchill Group at The Jackson Laboratory (Linux, Windows)
• BRB ArrayTools (MS Excel add-in) from National Cancer Institute (Windows)
• SAM MS Excel add-on from Stanford (Windows)
• SNOMAD from Pevsner Lab at Johns Hopkins School of Medicine (WEB)
• VERA and SAM from the Institute for Systems Biology (Unix/Linux, Windows)

• ArrayStat from Imaging Research, Inc (Windows)
• GeneSpring from Silicon Genetics (Linux, Windows, Mac)
• Acuity from Axon Instruments (Windows)
• SpotFire from SpotFire (Windows)

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• MeV: MultiExperiment Viewer from TIGR (Windows)
• Genesis from Graz University of Technology (Windows)
• CLUSFAVOR from Baylor College of Medicine (Windows)
• Cluster and Treeview from Michael Eisen's Lab (Windows)
• DNA-arrays analysis tools (various tools) from Spanish National Cancer Center (WEB)
• Expression Profiler (various tools) from EBI (WEB)
• GeneCluster from Broad Institute (UNIX, Windows)
• MAExplorer from NCI LEBC (UNIX/Linux, Windows, Mac, Mac OSX)
• XCluster from Stanford (Unix/Linux, Windows, Mac)

• GeneSpring from Silicon Genetics (Linux, Windows, Mac)
• Acuity from Axon Instruments (Windows)
• SpotFire from SpotFire (Windows)
• Genowiz from Ocimunbio
• J-Express from MolMine (Windows)
• arraySCOUT from Lion Biosciences (UNIX, Windows)
• GeneSight from BioDiscovery (Windows)
• PathwayAssist from Stratagene
• Rosetta Resolver System from Rosetta Biosoftware (Unix)
• Xpression from Invitrogen (Windows)

• GEO at NCBI
• AMAD flatfile database from UCSF (Unix/Linux, Windows, Mac web servers)
• ArrayDB from NHGRI ((Unix/Linux web server)
• BASE from Lund University (Linux/MySQL)
• Longhorn (LAD) from UT Austin
• GeneX-Lite and GeneX Server from NCGR
• MADAM: MicroArray DAta Manager from TIGR
• maxd from Manchester Bioinformatics (Unix/Linux)
• NOMAD from UCSF (Unix/Linux, Mac OSX)

• Acuity from Axon Instruments (Windows)
• PARTISAN arrayLIMS from ClonDiag (Unix)
• GeNet from Silicon Genetics