article Open AccessTop 1% cited
affy—analysis of <i>Affymetrix GeneChip</i> data at the probe level
Bioinformatics · 2004 · Vol. 20(3) · pp. 307–315
Laurent Gautier✉(Technical University of Denmark)Leslie Cope(Johns Hopkins University)Benjamin M. Bolstad(University of California, Berkeley)Rafael A. Irizarry(Johns Hopkins University)
Abstract
The affy package is an R package of functions and classes for the analysis of oligonucleotide arrays manufactured by Affymetrix. The package is currently in its second release, affy provides the user with extreme flexibility when carrying out an analysis and make it possible to access and manipulate probe intensity data. In this paper, we present the main classes and functions in the package and demonstrate how they can be used to process probe-level data. We also demonstrate the importance of probe-level analysis when using the Affymetrix GeneChip platform.
Gene expression and cancer classificationMolecular Biology Techniques and ApplicationsGenomics and Chromatin DynamicsComputer scienceGene chip analysisR packageFlexibility (engineering)Data miningFocus (optics)Data processingProcess (computing)Computational biologyDatabase
MeSH terms
AlgorithmsSoftwareUser-Computer InterfaceDNA ProbesDatabases, BibliographicInformation Storage and RetrievalSequence AlignmentSequence Analysis, DNAOligonucleotide Array Sequence AnalysisGene Expression ProfilingDatabases, Genetic
Funding
- Johns Hopkins University
Citations
5,411
FWCI
24.02
field-weighted impact
References
19
Percentile
100%
vs. same field & year
Citations per year
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References
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Bioinformatics · 2003 · 8,399 citations
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Cancer Cell · 2002 · 2,523 citations
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Nature Biotechnology · 1996 · 2,847 citations
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