title: CARMAweb: comprehensive R- and bioconductor-based web service for microarray data analysis.
abstract: 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.
authors.affiliation: Institute for Genomics and Bioinformatics, Graz University of Technology, Petersgasse 14, 8010 Graz, Austria.
authors.forename: Johannes
authors.initials: J
authors.lastname: Rainer
authors.forename: Fatima
authors.initials: F
authors.lastname: Sanchez-Cabo
authors.forename: Gernot
authors.initials: G
authors.lastname: Stocker
authors.forename: Alexander
authors.initials: A
authors.lastname: Sturn
authors.forename: Zlatko
authors.initials: Z
authors.lastname: Trajanoski
mesh_terms: D016000:Cluster Analysis; D003196:Computer Graphics; D020869:Gene Expression Profiling / Q000379:methods*; D020407:Internet; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D012984:Software; D014584:User-Computer Interface; D018875:Vocabulary, Controlled