Data analysis
Reviews/books/tutorials on microarray data analysis
- SIRU - DNA Microarray Analysis: Finnish IT centre for science (FREE!)
- 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
- Knudson - Guide to Analysis of DNA Microarray Data (Bioconductor): Knudsen, S
- Knudson - Guide to Analysis of DNA Microarray Data (R): Knudsen, S
- Venables - Modern Applied Statistics with S: Venables, VW
Image Analysis for Spotted cDNA/Oligo Arrays
- Dapple - Jeremy Buhler
- FSCAN - Fluorescently Probed cDNA Microarry Analysis (P. J. Munson, V. V. Prabhu & L. Young)
- GridGrinder - Corning Incorporated
- Pscan - Peak quantification using Statistical Comparative ANalysis (P. J. Munson, V. V. Prabhu & L. Young)
- ScanAlyze2 - Eisen Laboratory
- SpotFinder - The Institute for Genomic Research
- 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
- VSN - Variance Stabilising Normalisation in Bioconductor
- Limma - Linear Models for Microarray Data in Bioconductor
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:
- PLMImageGallery - Artifacts observed in the pseudo-chip images produced by affyPLM
- RMAExpress - Stand-alone Windows/Linux package for RMA
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
- ExpressionProfiler - European Bioinformatics Institute
- GenMAPP - GenMAPP
- GeneCluster - GeneCluster
- GEPAS- Gene Expression Pattern Analysis Suite
- MeV - MultiExperimentViewer
- MCLUST - 'mclust' library in Bioconductor
- MULTIV - 'multiv' library in Bioconductor
