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Nucleic Acids Research 2006 34(Web Server issue):W498-W503; doi:10.1093/nar/gkl038
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© The Author 2006. Published by Oxford University Press. All rights reserved
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions@oxfordjournals.org

Article

CARMAweb: comprehensive R- and bioconductor-based web service for microarray data analysis

Johannes Rainer1,3, Fatima Sanchez-Cabo1, Gernot Stocker1, Alexander Sturn1 and Zlatko Trajanoski1,2,*

1 Institute for Genomics and Bioinformatics, Graz University of Technology Petersgasse 14, 8010 Graz, Austria 2 Christian-Doppler Laboratory for Genomics and Bioinformatics, Graz University of Technology Petersgasse 14, 8010 Graz, Austria 3 Tyrolean Cancer Research Institute Innrain 66, 6020 Innsbruck, Austria

*To whom correspondence should be addressed. Tel: +43 316 873 5332; Fax: +43 316 873 5340; Email: zlatko.trajanoski{at}tugraz.at

Received November 9, 2005. Revised December 23, 2005. Accepted January 10, 2006.

CARMAweb (Comprehensive R-based Microarray Analysis web service) is a web application designed for the analysis of microarray data. CARMAweb performs data preprocessing (background correction, quality control and normalization), detection of differentially expressed genes, cluster analysis, dimension reduction and visualization, classification, and Gene Ontology-term analysis. This web application accepts raw data from a variety of imaging software tools for the most widely used microarray platforms: Affymetrix GeneChips, spotted two-color microarrays and Applied Biosystems (ABI) microarrays. R and packages from the Bioconductor project are used as an analytical engine in combination with the R function Sweave, which allows automatic generation of analysis reports. These report files contain all R commands used to perform the analysis and guarantee therefore a maximum transparency and reproducibility for each analysis. The web application is implemented in Java based on the latest J2EE (Java 2 Enterprise Edition) software technology. CARMAweb is freely available at https://carmaweb.genome.tugraz.at.


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