Software

A-MADMAN: Annotation-based microarray data meta-analysis tool

Andrea Bisognin¹ , Alessandro Coppe¹ , Francesco Ferrari¹ , Davide Risso^1,2 , Chiara Romualdi¹ , Silvio Bicciato³ and Stefania Bortoluzzi¹

¹University of Padova, Department of Biology, Via G. Colombo 3, 35121, Padova, Italy

²University of Padova, Department of Statistical Sciences, via C. Battisti2 41, 35121 Padova, Italy

³University of Modena and Reggio Emilia, Department of Biomedical Sciences, Via G. Campi 287, 41100, Modena, Italy

author email corresponding author email

BMC Bioinformatics 2009, 10:201doi:10.1186/1471-2105-10-201

Published:	29 June 2009

Abstract

Background

Publicly available datasets of microarray gene expression signals represent an unprecedented opportunity for extracting genomic relevant information and validating biological hypotheses. However, the exploitation of this exceptionally rich mine of information is still hampered by the lack of appropriate computational tools, able to overcome the critical issues raised by meta-analysis.

Results

This work presents A-MADMAN, an open source web application which allows the retrieval, annotation, organization and meta-analysis of gene expression datasets obtained from Gene Expression Omnibus. A-MADMAN addresses and resolves several open issues in the meta-analysis of gene expression data.

Conclusion

A-MADMAN allows i) the batch retrieval from Gene Expression Omnibus and the local organization of raw data files and of any related meta-information, ii) the re-annotation of samples to fix incomplete, or otherwise inadequate, metadata and to create user-defined batches of data, iii) the integrative analysis of data obtained from different Affymetrix platforms through custom chip definition files and meta-normalization. Software and documentation are available on-line at http://compgen.bio.unipd.it/bioinfo/amadman/ webcite.