Robust estimators for expression analysis

By Earl Hubbell, Wei‐Min Liu, Rui Mei. Bioinform., 2002

660 citations recorded by the source corpus.

Subfields: Management Science and Operations Research, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/9965f9869d39d1375cf8d6329ea08001f579e973

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Management Science and Operations Research

1. Ann Nowé
2. Sorin Draghici
3. Hugues Bersini
4. Purvesh Khatri
5. Cosmin Lazar
6. Julian Reiss

In Molecular Biology

1. Purvesh Khatri
2. Sorin Draghici
3. Magali Olivier
4. M. Hollstein
5. A. Bar‐Even
6. Ann Nowé
7. Rui Mei
8. Doron Lancet

Citations in the corpus

• Rosetta error model for gene expression analysis (2006, background): “The background noise mean and variance are denoted by: ( ) ( ) ).,(),( ),(),( 2 jijiVar jijiE bkgbkg bkgbkg σε µε = = The cross-hybridization noise has its mean and variance as well: ( ) ( ) ),(),( ),(),( 2 jijiVar jijiE xhybxhyb ijxhybxhyb σε φβµε = ⋅≈= where βj is the overall non-specific binding…”
• Genome-wide midrange transcription profiles reveal expression level relationships in human tissue specification (2005, methodology): “0) software (Hubbell et al. 2002; Liu et al. 2003) with default parameters, without using the MAS 5.”
• Batch effect removal methods for microarray gene expression data integration: a survey (2013, methodology): “We assume that the gene expression data have been log-transformed and preprocessed (using either MAS5 [31], RMA [32], fRMA [33] for Affymetrix platforms or the preprocessing tools provided by ‘lumi’ Bioconductor package for Illumina platforms [34]) for background correction, normalization and…”
• Reliability and reproducibility issues in DNA microarray measurements. (2006, background): “True concentrations can be obtained by either spike-in or dilution experiments [ 24 ] or measuring transcript levels by independent means, for example, quantitative RT–PCR or northern blots.”
• TP53 Variations in Human Cancers: New Lessons from the IARC TP53 Database and Genomics Data (2016, background): “All mRNA expression values are MAS5 normalized, with a 2% trimmed mean of 150 [Hubbell et al., 2002].”
• Analysis of high density expression microarrays with signed-rank call algorithms (2002, methodology): “The accompanying paper Hubbell et al. (2002) describes the computation of microarray signals based on Tukey’s biweight estimation.”