Data analysis
Reviews/books/tutorials on microarray data analysis
- Russell - Microarray Technology in Practice: Russell, S., Meadows, L.M., Russell, R.R.
- Stekel - Microarray Bioinformatics: Stekel, D
- Parmigiani - The analysis of gene expression data: methods and software
- Draghici - Data Analysis Tools for DNA Microarrays: Draghici, S
- Kickstart - Kickstart R
- Helden - Statistical Analysis of Microarray Data: van Helden, J
Image Analysis for Spotted cDNA/Oligo Arrays
- Dapple - Jeremy Buhler
- FSCAN - Fluorescently Probed cDNA Microarry Analysis (P. J. Munson, V. V. Prabhu & L. Young)
- Pscan - Peak quantification using Statistical Comparative ANalysis (P. J. Munson, V. V. Prabhu & L. Young)
- ScanAlyze2 - Eisen Laboratory
- Spot - Jain Laboratory
Data Normalisation for Spotted cDNA/Oligo Arrays
- CARMAweb - Comprehensive R based Microarray Analysis web frontend
- GEPAS- Gene Expression Pattern Analysis Suite
- MIDAS - Microarray Data Analysis System
- SAM - Significance Analysis of Microarrays
- SNOMAD - Standardisation & Normalisation of Microarray Data
- YASMA - Yet Another Statistical Microarray Analysis
- FSPMA - Friendly Statistics Toolbox for Microarray Analysis
- Limma - Linear Models for Microarray Data in Bioconductor
- VSN - Variance stablization and normlization
Data Normalisation for Affymetrix Arrays
- AffyComp - Benchmark for Affy expression measures: a comparison of various tools
- AFFY - 'affy' library in Bioconductor: MAS5, MBEI, RMA
- affyPLM - 'affyPLM' library in Bioconductor: probe level models (PLM)
- CARMAweb - Comprehensive R based Microarray Analysis web frontend
- GEPAS- Gene Expression Pattern Analysis Suite
- dChip - DNA-Chip Analyzer
- FSPMA - Friendly Statistics Toolbox for Microarray Analysis
- GCRMA - 'gcrma' library in Bioconductor:
Statistical Analysis for Affymetrix & Spotted cDNA/Oligo Arrays
- CARMAweb - Comprehensive R based Microarray Analysis web frontend
- CyberT - Cyber-T
- FSPMA - Friendly Statistics Toolbox for Microarray Analysis
- GenePublisher - GenePublisher
- GEPAS- Gene Expression Pattern Analysis Suite
- MeV - MultiExperimentViewer
- SAM - Significance Analysis of Microarrays
- YASMA - Yet Another Statistical Microarray Analysis
- Limma - Linear Models for Microarray Data in Bioconductor
Higher level Analysis for Affymetrix & Spotted cDNA/Oligo Arrays
- Eisen - Cluster and Treeview
- GenePattern - GenePattern
- GEPAS- Gene Expression Pattern Analysis Suite
- MeV - MultiExperimentViewer
- MCLUST - 'mclust' library in Bioconductor
