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Related Experiment Video

Updated: May 20, 2026

Comprehensive Workflow for the Genome-wide Identification and Expression Meta-analysis of the ATL E3 Ubiquitin Ligase Gene Family in Grapevine
10:40

Comprehensive Workflow for the Genome-wide Identification and Expression Meta-analysis of the ATL E3 Ubiquitin Ligase Gene Family in Grapevine

Published on: December 22, 2017

AMDA 2.13: A major update for automated cross-platform microarray data analysis.

Dimos Kapetis1, Ferdinando Clarelli, Federico Vitulli

  • 1Genopolis-Consortium for Functional Genomics, Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy. dimos.kapetis@istituto-besta.it

Biotechniques
|July 18, 2012
PubMed
Summary
This summary is machine-generated.

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The Automated Microarray Data Analysis (AMDA) pipeline was updated to version 2.13, offering enhanced multi-platform support for diverse microarray data analysis. This improved tool provides better quality control, advanced filtering, and pathway mapping for deeper biological insights.

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • Microarray analysis requires sophisticated pipelines for data pre-processing, normalization, differential gene expression analysis, clustering, and functional annotation.
  • The Automated Microarray Data Analysis (AMDA) version 2.3.5 was previously developed for Affymetrix 3' IVT GeneChips.

Purpose of the Study:

  • To develop an updated, multi-platform version of the AMDA pipeline (AMDA 2.13) to accommodate newer technologies and open-source tool demands.
  • To enhance the functionality and user-friendliness of the AMDA pipeline for broader microarray data analysis applications.

Main Methods:

  • AMDA 2.13 incorporates advanced quality control metrics and introduces annotation-driven (NetAffx) and signal-driven (Inter-Quartile Range) gene filtering.
  • The pipeline integrates approaches for experimental design and maps differentially expressed genes into KEGG pathways for enhanced biological interpretation.

Related Experiment Videos

Last Updated: May 20, 2026

Comprehensive Workflow for the Genome-wide Identification and Expression Meta-analysis of the ATL E3 Ubiquitin Ligase Gene Family in Grapevine
10:40

Comprehensive Workflow for the Genome-wide Identification and Expression Meta-analysis of the ATL E3 Ubiquitin Ligase Gene Family in Grapevine

Published on: December 22, 2017

  • AMDA 2.13 supports analysis across multiple platforms, including Affymetrix (cartridges, plates, Gene 1.0/1.1 ST, Exon 1.0 ST), Illumina Bead Arrays, and Agilent 4×44 arrays.

    • Main Results:

    • The updated AMDA 2.13 pipeline provides robust analysis for a wider range of microarray platforms compared to previous versions.
    • Enhanced quality control, flexible gene filtering options, and KEGG pathway mapping lead to more insightful biological data interpretation.
    • The new version features a more stable and user-friendly interface, supporting diverse experimental designs.

    Conclusions:

    • AMDA 2.13 represents a significant advancement in microarray data analysis, offering comprehensive support for multiple platforms and experimental designs.
    • The pipeline facilitates deeper biological understanding through improved data processing, insightful analysis modules, and up-to-date annotations.
    • AMDA 2.13 is a valuable open-source tool for researchers utilizing diverse microarray technologies.