Differential Expression Analysis of Complex RNA-seq Experiments Using edgeR ∗

@inproceedings{Chen2014DifferentialEA,
  title={Differential Expression Analysis of Complex RNA-seq Experiments Using edgeR ∗},
  author={Yunshun Chen and Aaron T. L. Lun and Gordon K. Smyth},
  year={2014}
}
This article reviews the statistical theory underlying the edgeR software package for differential expression of RNA-seq data. Negative binomial models are used to capture the quadratic mean-variance relationship that can be observed in RNA-seq data. Conditional likelihood methods are used to avoid bias when estimating the level of variation. Empirical Bayes methods are used to allow gene-specific variation estimates even when the number of replicate samples is very small. Generalized linear… CONTINUE READING

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