Shrinkage estimation of dispersion in Negative Binomial models for RNA-seq experiments with small sample size.

ABSTRACT:

Motivation

RNA-seq experiments produce digital counts of reads that are affected by both biological and technical variation. To distinguish the systematic changes in expression between conditions from noise, the counts are frequently modeled by the Negative Binomial distribution. However, in experiments with small sample size, the per-gene estimates of the dispersion parameter are unreliable.

Method

We propose a simple and effective approach for estimating the dispersions. First, we obtain the initial estimates for each gene using the method of moments. Second, the estimates are regularized, i.e. shrunk towards a common value that minimizes the average squared difference between the initial estimates and the shrinkage estimates. The approach does not require extra modeling a

SUBMITTER: Yu D 

PROVIDER: S-EPMC3654711 | biostudies-literature | 2013 May

REPOSITORIES: biostudies-literature