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Microarray Links
Online Data Analysis Tools
| Sample Size Calculation | NetAffx GO Mining (free login required) |
| CyberT (Stat program) | GenePublisher |
| GeneCruiser | Venny |
| Affy Regional Bias QC | GenePattern |
| RINdb |
| Onto Express | FatiGO |
| Gostat | GoToolBox |
| Panther | Ontologizer |
| List of GO analysis tools | DAVID |
| BiNGO |
Academic Data Analysis Software
| Public Domain Programs for MA Analysis | Cytoscape |
| Hierarchical Clustering Explorer | CRLMM (SNP genotyping algorithm) |
| Chipster | The Bio-Array Resource for Arabidopsis Functional Genomics |
| iArray Analyzer | CNAG |
| Expander | GSEA |
| SAM | DAVID (biological interpretation) |
| PowerArray | BRB ArrayTools |
| ATHENA | MAT (Model based Analysis of Tiling arrays) |
| Data Assist (for TaqMan RT-PCR data) | Affymetrix Integrated Genome Browser (IGB) |
| Q-value | BiNGO |
| CisGenome | TileMapper |
| TAS | MatchMiner |
Pathway Resources
| SABiosciences | GeneAssist Pathway Atlas |
| Calbiochem | Sigma-Aldrich Search Your Favorite Gene |
London Regional Core Facilities
| London Regional Proteomics Centre | Translational Research Centre |
| London Regional Transgenic and Gene Targeting Facility | |
List Servers
| Microarray listserver | GeneSpring |
| dChip | BioConductor |
| qPCR Forum | SEQAnswers |
Commercial Data Analysis Software
| Partek Genomics Suite | GeneSpring GT |
| Biotique's X-Ray | GeneSpring GX |
| ArrayVision | Golden Helix |
Selected Reading
Barr, Gordon A., Gao, Puhong. 2005. Issues for Consideration in the Analysis of Microarray Data in Behavioural Studies. Addition Biology 10,15-21 (March 2005).
Affymetrix. 2004. Sample Pooling for Microarray Analysis: A Statistical Assessment of Risks and Biases. Affymetrix.
Affymetrix. 2003. GeneChip Expression Analysis: Experimental Design, Statistical Analysis and Biological Interpretation. Affymetrix.
Affymetrix. 2003. Data Analysis Fundamentals Manual. Affymetrix.
Affymetrix. 2002. Statistical Algorithms Description Document Affymetrix.
Causton, C. Helen, Quackenbush, J. and Brazma A. 2003. Microarray Gene Expression Data Analysis: A Beginner's Guide. Blackwell Publishing.
Dudoit, S., Gentleman, R.C., and Quackenbush, J. 2003. Open Source Software for the Analysis of Microarray Data. BioTechniques 34:S45-S51 (March 2003).
Knudsen, S., 2002. A Biologist's Guide To Analysis of DNA Microarray Data. John Wiley & Sons, Inc.
Microarray Expression Data Analysis References
John C. Rockett and Gary M. Hellmann. 2004. Confirming Microarray Data - Is It Realy Necessary? Genomics. 2004 Apr;83(4):541-9.
Yee Hwa Yang and Terry Speed. 2002. Design Issues For cDNA Microarray Experiments. Nature Reviews: Genetics. 2002 Aug;
Priti Hegde, Rong Qi, Kristie Abernathy, Cheryl Gay, Sonia Dharap, Renee Gaspard, Julie Earle-Hughes, Erik Snesrud, Norman Lee, and John Quackenbush. 2000. A Concise Guide to cDNA Microarray Analysis. Biotechniques 29(3):548-50,552-4 (Sep. 2000) passim. Review.
Equipment & Reagent Suppliers
| Affymetrix | Agilent 2100 Bioanalyzer |
| Ambion RNA 6000 Ladder | Enzo BioArray High Yield RNA Transcript Labelling kit |
| Qiagen RNeasy kit | Genisphere |
Next-Generation Sequencing Resources
| Alignment algorithms | Alignment Visualization software |
| SeqAnswers | SeqAnswers software list |
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Site designed by Ericka Simon
Maintained by David
Carter
Last update: Sunday, August 22, 2010