1. AMarge: Automated Extensive Quality Assessment of Affymetrix chips.
- Author
-
Lozano JJ and Kalko SG
- Subjects
- Computer Simulation, Internet, Linear Models, Quality Control, Reproducibility of Results, Sensitivity and Specificity, Algorithms, Gene Expression Profiling methods, Models, Genetic, Oligonucleotide Array Sequence Analysis methods, Quality Assurance, Health Care methods, Software
- Abstract
Unlabelled: AMarge is a web tool for the automatic quality assessment of Affymetrix GeneChip data. It is essential to have a trustworthy set of chips in order to derive gene expression data for phenotypic analysis, and AMarge provides a complete and rigorous web-accessible tool to fulfill this need. The quality assessment steps include image plots of weights derived from a robust linear model fit of the data, a 3'/5' RNA digestion plot, and Affymetrix Microarray Suite version 5.0 (MAS 5.0) quality standard procedures. Furthermore, robust multi-array average expression values are generated in order to have a start-up expression set for the subsequent analysis. The results of the complete analysis are summarised and returned as an HTML report., Availability: The AMarge web interface is accessible at http://nin.crg.es/cgi-binf/AMargeWeb.cgi. A mirror server is also available at http://bioinformatics.istge.it/AMarge-bin/AMargeWeb.cgi. The software implementing all these methods is part of the Bioconductor project (http://www.bioconductor.org).
- Published
- 2006
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