Model-based analysis of oligonucleotide arrays: expression index computation and outlier detection.

By Cheng Li, W. Wong. Proceedings of the National Academy of Sciences of the United States of America, 2001

3,381 citations recorded by the source corpus.

View Paper: https://www.semanticscholar.org/paper/c86900fc9f326e9861adc395c7e4be93dcdb8c2c

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Citations in the corpus

Frozen robust multiarray analysis (fRMA). (2010, methodology): “First, we assessed the preprocessing algorithms in terms of accuracy, precision, and overall performance as done by “affycomp” and “spkTools” (Irizarry and others , 2006; McCall and Irizarry, 2008).”
Empirical Bayes Analysis of a Microarray Experiment (2001, methodology): “(2000) used a normal theory version of this idea, as, less directly, did Li and Wong (2000). Newton et al. (2000) focused on Gamma models.”
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].”
Comparison of Affymetrix GeneChip expression measures (2006, neutral): “dChip denotes the P M -only version of the algorithm described by Li and Wong (2001) .”
Ontology-Based Meta-Analysis of Global Collections of High-Throughput Public Data (2010, methodology): “Otherwise, expression summary intensities, such as those processed generated by MAS5 (Affymetrix) or dChip were processed [37].”
Integrating high-throughput and computational data elucidates bacterial networks (2004, methodology): “The image files were processed and expression values were normalized using dChip softwar”
Bioconductor: open software development for computational biology and bioinformatics (2004, methodology): “Examples include the Spot system [9], MAANOVA [10] and dChip [11].”
Neuronal and glioma-derived stem cell factor induces angiogenesis within the brain. (2006, methodology): “By dChip software (Li and Wong, 2001), the CEL files were normalized to a median-intensity array, and model-based expression values were calculated using PM/MM difference model.”
Gene Expression Profiling of Gliomas Strongly Predicts Survival (2004, methodology): “were uploaded into the dCHIP program (22) and normalized to the median”
A gene expression atlas of the model legume Medicago truncatula. (2008, methodology): “The fraction of genes for which transcripts were detected (called ‘present’ by dCHIP; Li and Wong, 2001) was similar in all samples, and ranged”
A comparative review of statistical methods for discovering differentially expressed genes in replicated microarray experiments (2002, methodology): “The gene expression levels may have been suitably preprocessed, including dimension reduction, data normalization and data transformation (e.g. Dudoit et al. , 2000; Efron et al. , 2000; Li and Wong, 2001; Kerr et al. , 2000; Yang et al. , 2000).”
On parametric empirical Bayes methods for comparing multiple groups using replicated gene expression profiles (2003, methodology): “DNA chip analyser [21] was used here, but many other methods are available.”
Fundamentals of cDNA microarray data analysis. (2003, background): “ship between signal intensity and transcript abundance [56,57], probespecific biases [ 58 ] and normalization across different arrays [55,56].”
Microarray data normalization and transformation (2002, background): “For example, there are specific transformations that have been developed for analysis of data from particular platform”
Robust computational reconstitution – a new method for the comparative analysis of gene expression in tissues and isolated cell fractions (2006, methodology): “[16]; and 4) Model Based Expression Index (MBEI) of Li and Wong [17] as implemented in R and the GenePublisher web-interface [37].”
Mutational loss of PTEN induces resistance to NOTCH1 inhibition in T-cell leukemia (2007, neutral): “Interarray intensity differences were normalized with Dchi”