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

被引：180
作者：
Rainer, Johannes
Sanchez-Cabo, Fatima
Stocker, Gernot
Sturn, Alexander
Trajanoski, Zlatko
机构：
[1] Graz Univ Technol, Inst Genom & Bioinformat, A-8010 Graz, Austria
[2] Graz Univ Technol, Christian Doppler Lab Genom & Bioinformat, A-8010 Graz, Austria
[3] Univ Innsbruck, Tyrolean Canc Res Inst, A-6020 Innsbruck, Austria
来源：
NUCLEIC ACIDS RESEARCH | 2006年 / 34卷
关键词：
D O I：
10.1093/nar/gkl038
中图分类号：
Q5 [生物化学]; Q7 [分子生物学];
学科分类号：
071010 ; 081704 ;
摘要：
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.
引用
收藏
页码：W498 / W503
页数：6
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