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2013 ; 22
(5
): 519-36
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Finding consistent patterns: a nonparametric approach for identifying
differential expression in RNA-Seq data
#MMPMID22127579
Li J
; Tibshirani R
Stat Methods Med Res
2013[Oct]; 22
(5
): 519-36
PMID22127579
show ga
We discuss the identification of features that are associated with an outcome in
RNA-Sequencing (RNA-Seq) and other sequencing-based comparative genomic
experiments. RNA-Seq data takes the form of counts, so models based on the normal
distribution are generally unsuitable. The problem is especially challenging
because different sequencing experiments may generate quite different total
numbers of reads, or 'sequencing depths'. Existing methods for this problem are
based on Poisson or negative binomial models: they are useful but can be heavily
influenced by 'outliers' in the data. We introduce a simple, non-parametric
method with resampling to account for the different sequencing depths. The new
method is more robust than parametric methods. It can be applied to data with
quantitative, survival, two-class or multiple-class outcomes. We compare our
proposed method to Poisson and negative binomial-based methods in simulated and
real data sets, and find that our method discovers more consistent patterns than
competing methods.