Exploration, normalization, and summaries of high density oligonucleotide array probe level data.

By Rafael A. Irizarry, Bridget G. Hobbs, François Collin, Y. Beazer-Barclay, Kristen J Antonellis, U. Scherf, Terence P. Speed. Biostatistics, 2003

11,051 citations recorded by the source corpus.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/a5e6f4ed864385bab62e577984cfa3d5ebc66036

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Citations in the corpus

Batch effect removal methods for microarray gene expression data integration: a survey (2013, methodology): “Quantile normalization (QN) is more frequently used for normalization at the probe level (see RMA preprocessing algorithm [32]), but it has been also used explicitly for batch effect removal [48, 49].”
Modeling Oncogenic Signaling in Colon Tumors by Multidirectional Analyses of Microarray Data Directed for Maximization of Analytical Reliability (2010, background): “0 [36], MBEI [37], RMA [38], and GCGMA [39].”
HIF-1-mediated expression of pyruvate dehydrogenase kinase: a metabolic switch required for cellular adaptation to hypoxia. (2006, methodology): “…signals, data analysis was conducted on the microarrays’ CEL file probe signal values at the Affymetrix probe pair (perfect match [PM] probe and mismatch [MM] probe) level, using the statistical algorithm Robust Multiarray Analysis (RMA) (Irizarry et al., 2003) with the bioconductor package Affy.”
Multiple Hypothesis Testing by Clustering Treatment Effects (2007, methodology): “The data was background-corrected and normalized using the robust multichip averaging (RMA) method of Irizarry et al. (2003) as implemented in the affy package of BioConductor (Gentleman et al. 2004).”
A benchmark for Affymetrix GeneChip expression measures (2004, methodology): “Similar or even identical descriptive methods have been used by a variety of researchers to evaluate measures of expression (Holder et al., 2001; Workman et al., 2002; Irizarry et al., 2003a; Naef et al., 2001; Li and Wong, 2001).”
PageMan: An interactive ontology tool to generate, display, and annotate overview graphs for profiling experiments (2006, methodology): “The RMA expression values for the samples were calculated [20] and a linear model was fitted using BioConductor [15,21].”
A scaling normalization method for differential expression analysis of RNA-seq data (2010, neutral): “The assumptions behind the TMM method are similar to the assumptions commonly made in microarray normalization procedures such as lowess normalization [21] and quantile normalization [22].”
Myc Stimulates Nuclearly Encoded Mitochondrial Genes and Mitochondrial Biogenesis (2005, methodology): “The image data were processed with the statistical procedure Robust Multiarray Analysis to obtain gene expression signals ( 22 ), and statistically significant changes in gene expression was obtained with an empirical Bayes method using gamma-gamma or log normalnormal modeling (35).”
ATTED-II: a database of co-expressed genes and cis elements for identifying co-regulated gene groups in Arabidopsis (2006, methodology): “The profiles were constructed from 1388 GeneChip data downloaded from TAIR (4), which were manually divided into 53 experimental groups and normalized by RMA method (39).”
Cytosolic Ascorbate Peroxidase 1 Is a Central Component of the Reactive Oxygen Gene Network of Arabidopsisw⃞ (2005, methodology): “All GeneChip arrays were processed first by robust multiarray average (RMA) (Irizarry et al., 2003) using the R package affy (Gautier et al., 2004).”
Elucidation of the phenotypic, functional, and molecular topography of a myeloerythroid progenitor cell hierarchy. (2007, methodology): “For subsequent analysis, probe level expression values were extracted by using RMA (Irizarry et al., 2003), and subsequent analyses were performed with dChip software (http://biosun1.harvard.edu/complab/dchip/) after filtering (0.5 SD/mean 1,000).”