MOTIVATION: The processing of the Affymetrix GeneChip data has been a recent focus for data analysts. Alternatives to the original procedure have been proposed and some of these new methods are widely used. RESULTS: 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.
MOTIVATION: The processing of the Affymetrix GeneChip data has been a recent focus for data analysts. Alternatives to the original procedure have been proposed and some of these new methods are widely used. RESULTS: 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.
Authors: Adam S Crystal; Alice T Shaw; Lecia V Sequist; Luc Friboulet; Matthew J Niederst; Elizabeth L Lockerman; Rosa L Frias; Justin F Gainor; Arnaud Amzallag; Patricia Greninger; Dana Lee; Anuj Kalsy; Maria Gomez-Caraballo; Leila Elamine; Emily Howe; Wooyoung Hur; Eugene Lifshits; Hayley E Robinson; Ryohei Katayama; Anthony C Faber; Mark M Awad; Sridhar Ramaswamy; Mari Mino-Kenudson; A John Iafrate; Cyril H Benes; Jeffrey A Engelman Journal: Science Date: 2014-11-13 Impact factor: 47.728
Authors: Charles R Farber; Scott A Kelly; Ethan Baruch; Daniel Yu; Kunjie Hua; Derrick L Nehrenberg; Fernando Pardo-Manuel de Villena; Ryan J Buus; Theodore Garland; Daniel Pomp Journal: J Bone Miner Res Date: 2011-09 Impact factor: 6.741
Authors: Divya Chandran; Yu Chuan Tai; Gregory Hather; Julia Dewdney; Carine Denoux; Diane G Burgess; Frederick M Ausubel; Terence P Speed; Mary C Wildermuth Journal: Plant Physiol Date: 2009-01-28 Impact factor: 8.340
Authors: Angelical S Martin; Dennis M Abraham; Kathleen A Hershberger; Dhaval P Bhatt; Lan Mao; Huaxia Cui; Juan Liu; Xiaojing Liu; Michael J Muehlbauer; Paul A Grimsrud; Jason W Locasale; R Mark Payne; Matthew D Hirschey Journal: JCI Insight Date: 2017-07-20
Authors: Gerald W Tannock; Corinda Taylor; Blair Lawley; Diane Loach; Maree Gould; Amy C Dunn; Alexander D McLellan; Michael A Black; Les McNoe; James Dekker; Pramod Gopal; Michael A Collett Journal: Appl Environ Microbiol Date: 2014-02-28 Impact factor: 4.792
Authors: Giuseppe Matarese; Claudia La Rocca; Hyun-Seuk Moon; Joo Young Huh; Mary T Brinkoetter; Sharon Chou; Francesco Perna; Dario Greco; Holly P Kilim; Chuanyun Gao; Kalliope Arampatzi; Zhaoxi Wang; Christos S Mantzoros Journal: Proc Natl Acad Sci U S A Date: 2013-02-04 Impact factor: 11.205