An Iterative Leave-One-Out Approach to Outlier Detection in RNA-Seq Data

The discrete data structure and large sequencing depth of RNA sequencing (RNA-seq) experiments can often generate outlier read counts in one or more RNA samples within a homogeneous group. Thus, how to identify and manage outlier observations in RNA-seq data is an emerging topic of interest. One of the main objectives in these research efforts is to develop statistical methodology that effectively balances the impact of outlier observations and achieves maximal power for statistical testing. To reach that goal, strengthening the accuracy of outlier detection is an important precursor. Current outlier detection algorithms for RNA-seq data are executed within a testing framework and may be sensitive to sparse data and heavy-tailed distributions. Therefore, researchers from the FDA’s National Center for Toxicological Research, propose a univariate algorithm that utilizes a probabilistic approach to measure the deviation between an observation and the distribution generating the remaining data and implement it within in an iterative leave-one-out design strategy. Analyses of real and simulated RNA-seq data show that the proposed methodology has higher outlier detection rates for both non-normalized and normalized negative binomial distributed data.


Availability – The R code for running iLOO is available at: S1 R Code.

George NI, Bowyer JF, Crabtree NM, Chang CW. (2015) An Iterative Leave-One-Out Approach to Outlier Detection in RNA-Seq Data. PLoS One 10(6):e0125224. [article]

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