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Chip Definition Files CDF

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Encodes the physical design of the microarray and contain the sequence details to link the oligonucleotide probes of the chip to the interrogated transcripts. CDFs is a set of custom for Affymetrix human GeneChips, based on the information contained in the GeneAnnot database. This method solves the problem of a reliable reconstruction of expression levels and eliminate the existence of more than one probeset per gene, which often leads to discordant expression signals for the same transcript when gene differential expression is the focus of the analysis.

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CDF forum

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CDF classification

CDF specifications

Software type:
Package/Module
Restrictions to use:
None
Programming languages:
R
Computer skills:
Advanced
Stability:
Stable
Maintained:
Yes
Interface:
Command line interface
Operating system:
Unix/Linux, Windows
License:
GNU General Public License version 3.0
Version:
2.2.1
Source code URL:
http://www.xlab.unimo.it/GA_CDF/paper_DATA/SupplementaryFile1.txt

CDF distribution

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No versioning.

CDF support

Maintainer

  • Silvio Bicciato <>

Credits

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Publications

Institution(s)

Department of Biomedical Sciences, University of Modena and Reggio Emilia, Modena, Italy; Department of Biology, University of Padova, Padova, Italy; Department of Molecular Genetics, The Weizmann Institute of Science, Israel; Department of Biological Services, The Weizmann Institute of Science, Israel; Bioinformatics Knowledge Unit, The Lorry I. Lokey Interdisciplinary Center for Life Sciences and Engineering Technion, Israel Institute of Technology, Haifa, Israel; Department of Chemical Engineering Processes, University of Padova, Padova, Italy

Funding source(s)

This work was supported by grants from the Italian Ministry of University and Research (PRIN2005050779 and PRIN2005069853), OncoSuisse Collaborative Cancer Research (OCS-1939-8-2006), the University of Padova (CPDA065788/06, CPDR064110 and CPDR074285), Fondazione Cassa di Risparmio di Padova e Rovigo (Progetti di Eccellenza 2006), the Weizmann Institute of Science Crown Human Genome Center and the Abraham and Judith Goldwasser Fund.

Link to literature

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