AMDA 2.13: A major update for automated cross-platform microarray data analysis.
Microarray platforms require analytical pipelines with modules for data pre-processing including data normalization, statistical analysis for identification of differentially expressed genes, cluster analysis, and functional annotation. We previously developed the Automated Microarray Data Analysis (AMDA, version 2.3.5) pipeline to process Affymetrix 3' IVT GeneChips. The availability of newer technologies that demand open-source tools for microarray data analysis has impelled us to develop an updated multi-platform version, AMDA 2.13. It includes additional quality control metrics, annotation-driven (annotation grade of Affymetrix NetAffx) and signal-driven (Inter-Quartile Range) gene filtering, and approaches to experimental design. To enhance understanding of biological data, differentially expressed genes have been mapped into KEGG pathways. Finally, a more stable and user-friendly interface was designed to integrate the requirements for different platforms. AMDA 2.13 allows the analysis of Affymetrix (cartridges and plates) and whole transcript probe design (Gene 1.0/1.1 ST and Exon 1.0 ST GeneChips), Illumina Bead Arrays, and one-channel Agilent 4×44 arrays. Relative to early versions, it supports various experimental designs and delivers more insightful biological understanding and up-to-date annotations.
Genopolis-Consortium for Functional Genomics, Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy. dimos.kapetis@istituto-besta.it
Dimos
D
Kapetis
Ferdinando
F
Clarelli
Federico
F
Vitulli
Nicole Kerlero
NK
de Rosbo
Ottavio
O
Beretta
Maria
M
Foti
Paola
P
Ricciardi-Castagnoli
Francesca
F
Zolezzi
D020869:Gene Expression Profiling / Q000379:methods*; D023281:Genomics / Q000379:methods; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D012984:Software; D014584:User-Computer Interface