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It uses a negative binomial distribution to model total variation.
They employ a negative binomial distribution to model both biological and technical noise in the total counts of expressed genes.
DESeq uses a negative binomial distribution to model genic read counts following normalisation based on size factors and variance.
Because it was not, we used a Poisson, rather than a negative binomial, distribution to model the count outcome variables.
First, we analyzed the count data with the Bioconductor package edgeR[ 20], which uses the negative binomial distribution to model the count data.
Taking into account the over-dispersed distribution of RD values (Anders and Huber, 2010), we use a negative binomial distribution to model RD signals.
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Using beta binomial distributions to model predictions and errors works well, however, and the ratio of such distributions can be used to estimate the likelihood that a given prediction will be incorrect.
In principle, it is preferable to model the counts as a mixture of negative binomial distributions to model over dispersion of the count data.
Two other approaches: Maq (Li,H. et al., 2008) and SOAPSNP (Li,R. et al., 2008) have proposed using Binomial distributions to model genotypes; however, these were developed in the context of sequencing normal genomes, not cancer genomes.
We use a beta-binomial distribution to model the probability of the evidence, given a genotype that matches the reference.
Previous studies have used the beta-binomial distribution to model the count data underlying ASE measurements (e.g. Skelly et al. 2011).
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