Analysis of high density expression microarrays with signed-rank call algorithms

By Wei‐Min Liu, Rui Mei, X. Di, T. Ryder, Earl Hubbell, S. Dee, Teresa A. Webster, Christina A. Harrington, M. Ho, J. Baid and 1 more. Bioinform., 2002

475 citations recorded by the source corpus.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/bd37ef00c998eac4230e57521498b02cdb2b416f

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Citations in the corpus

GENEVESTIGATOR. Arabidopsis Microarray Database and Analysis Toolbox1[w] (2004, methodology): “Raw experimental data from users is processed using Affymetrix MAS 5.0 software to a target value (TGT) of 1,000 (Liu et al., 2002).”
Robust estimators for expression analysis (2002, methodology): “To deal with this, we apply the simplest statistical technique that allows us to fill-in the censored values, which is to impute appropriate values ( Little and Rubin, 1987 ).”
Bgee: Integrating and Comparing Heterogeneous Transcriptome Data Among Species (2008, methodology): “This method is implemented by the MAS5 software [17]; based on these statistical analyses, probesets are flagged as "present", "marginal", or "absent".”
Rosetta error model for gene expression analysis (2006, methodology): “Many data preprocessing methods, such as background-subtraction, normalization, detrending, and fluorescentreversal combination have been developed to reduce the impact of the systematic errors on gene-expression analyses (Schadt, et al., 2002; Yang, et al., 2002; Quackenbush, 2002).”
Large-scale prediction of long non-coding RNA functions in a coding–non-coding gene co-expression network (2011, methodology): “Genes were regarded as expressed under an experimental condition only if they were detected in 50% of all the replicated samples according to MAS5CALLS (27).”
Simpleaffy: a BioConductor package for Affymetrix Quality Control and data analysis (2005, methodology): “In addition, the MAS 5.0 algorithms for generating expression summaries (Hubbellet al., 2002) and for generating detection calls (Liu et al., 2002) have also been implemented in C, for speed.”
The Transcriptional Innate Immune Response to flg22. Interplay and Overlap with Avr Gene-Dependent Defense Responses and Bacterial Pathogenesis1[w] (2004, methodology): “Vol. 135, 2004 performed using Affymetrix software (see ‘‘Materials and Methods’’ for details and Liu et al., 2002).”