Stochastic Models Inspired by Hybridization Theory for Short Oligonucleotide Arrays

By Zhijin Wu, Rafael A. Irizarry. J. Comput. Biol., 2004

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Preferred analysis methods for Affymetrix GeneChips revealed by a wholly defined control dataset (2005, methodology): “In addition, we used the dChip [19], MAS 5.0 [12], Perfect Match [20,21] and SAM [27] executa-bles made available by the respective authors.”
A Model-Based Background Adjustment for Oligonucleotide Expression Arrays (2004, unknown): “Similar results for prediction of NSB are found in Wu and Irizarry (2004).”
From RNA-seq reads to differential expression results (2010, background): “It is well known that cross-hybridization of microarray probes affects expression measures in a nonuniform way [80,81] and sequence content influences measured probe intensities [82].”
CellMiner: a web-based suite of genomic and pharmacologic tools to explore transcript and drug patterns in the NCI-60 cell line set (2012, unknown): “Affymetrix microarrays were normalized by GCRMA (20).”