CDF pipeline

CDF specifications

Information


Unique identifier OMICS_14385
Name CDF
Alternative name Chip Definition Files
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Windows
Programming languages R
License GNU General Public License version 3.0
Computer skills Advanced
Version 2.2.1
Stability Stable
Source code URL http://www.xlab.unimo.it/GA_CDF/paper_DATA/SupplementaryFile1.txt
Maintained Yes

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Maintainer


  • person_outline Silvio Bicciato <>

Publication for Chip Definition Files

CDF IN pipeline

2016
PMCID: 5091760
PMID: 27806114
DOI: 10.1371/journal.pone.0166090

[…] analysis., the microarray raw data deposited in arrayexpress (accession e-mtab-4923) was preprocessed with the justrma function of the affy bioconductor package [42] with geneannot based custom cdf (gahgu133plus2 v2.2.1) [43]. the log-2 normalized intensities were adjusted for batch effects by using combat function of the sva bioconductor package [44]. the cmdscale function was used […]

CDF 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
CDF 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.

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