A-MADMAN: annotation-based microarray data meta-analysis tool.
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.


CONCLUSIONS
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/.
Bisognin
Andrea
A
University of Padova, Department of Biology, Padova, Italy. andrea.bisognin@gmail.com
Coppe
Alessandro
A
Ferrari
Francesco
F
Risso
Davide
D
Romualdi
Chiara
C
Bicciato
Silvio
S
Bortoluzzi
Stefania
S
D020869:Gene Expression Profiling; D020407:Internet; D015201:Meta-Analysis as Topic; D046228:Microarray Analysis / Q000379:methods*; D012984:Software