A comparison of normalization methods for high density oligonucleotide array data based on variance and bias

By Benjamin M. Bolstad, Rafael A. Irizarry, Magnus Åstrand, Terence P. Speed. Bioinform., 2003

8,656 citations recorded by the source corpus.

View Paper: https://www.semanticscholar.org/paper/6f3675caf5bcce3ad0f0414de0d19390cb6f14ea

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In Molecular Biology

Citations in the corpus

Multiple common variants for celiac disease influencing immune gene expression (2010, neutral): “We performed quantile normalization using the median rank distributio”
A multivariate empirical Bayes statistic for replicated microarray time course data (2006, methodology): “The array preprocessing were done using the Robust Multi-array Analysis (RMA) algorithm described in [ 5 , 18] which is implemented in the Bioconductor package affy.”
PAGE: Parametric Analysis of Gene Set Enrichment (2005, neutral): “For a given microarray data set, use of different methods of data preprocessing, array normalization, and statistical inference can lead to different end results [3,4,29].”
Context-Specific Metabolic Networks Are Consistent with Experiments (2008, methodology): “The data for human skeletal muscle was processed using the affy package [26] and the mas5calls function.”
Microarray data analysis: from disarray to consolidation and consensus (2006, methodology): “RMA and a modification of this method, GCRMA, often perform as well or better than competitors, although there is some controversy about which method is bes”
Social regulation of gene expression in human leukocytes (2007, methodology): “Robust multiarray averaging [60] was applied to quantify expression of the 22,283 assayed transcripts, and differentially expressed genes were identified as those showing ≥30% difference in mean expression levels in samples from high- versus low-lonely individuals (corresponding to a FDR of 10%) [59”
Exploration, normalization, and summaries of high density oligonucleotide array probe level data. (2003, methodology): “Bolstad et al. (2002) present a review of these methods and find quantile normalization to perform best.”
Data-analysis strategies for image-based cell profiling (2017, background): “The resulting compact representation is computationally more tractable, and it additionally avoids overrepresentation of similar features, that is, having a subgroup of features that measure similar or redundant properties of cells.”