Use of within-array replicate spots for assessing differential expression in microarray experiments

By Gordon K. Smyth, Joëlle Michaud, Hamish S. Scott. Bioinform., 2005

1,459 citations recorded by the source corpus.

View Paper: https://www.semanticscholar.org/paper/116fed4779c786c01b875cea7941a02380e63651

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Citations in the corpus

voom: precision weights unlock linear model analysis tools for RNA-seq read counts (2014, methodology): “For example, we often find it useful in our own microarray gene expression studies to estimate empirical quality weights to downweight poor quality RNA samples [29], or to use random effects to allow for repeated measures on the same experimental units [4, 5], or to conduct gene set tests for expres”
Highly Specific Gene Silencing by Artificial MicroRNAs in Arabidopsis[W][OA] (2006, methodology): “(E) Overlap of significantly downregulated genes using the Linear Model for Microarray Data (LIMMA) package (Smyth et al., 2005) or logit-T (in parentheses; Lemon et al., 2003) in lfy-12 and amiR-lfy-1 plants indicates a very similar molecular phenotype, with amiR-lfy-1 plants being on average…”
Analysis of Transcription Factor HY5 Genomic Binding Sites Revealed Its Hierarchical Role in Light Regulation of Development[W] (2007, methodology): “The linear model and statistical procedure were provided and implemented according to the limma package for R (Smyth et al., 2005).”
Neuroprotective effects of brain-derived neurotrophic factor in rodent and primate models of Alzheimer’s disease (2009, methodology): “We performed contrast analysis of differential expression with the Linear Models of Microarray (LIMMA) softwar”
limma powers differential expression analyses for RNA-sequencing and microarray studies (2015, methodology): “Originally the idea was used to estimate the correlation between replicate copies of the same probe on a microarray [65].”
Evaluation of time profile reconstruction from complex two-color microarray designs (2008, positive): “3) limmaQual, the Limma model [4,20,21] including an array quality adjustment:”