Identifying the differentially expressed genes with RNA-Seq data

Recently, the RNA-Seq experiment is developed for a high-throughput DNA sequencing method for mapping and quantifying the transcriptomes. The gene expression level obtained from a RNA-Seq experiment is of the count data type and is often fitted by a Negative-Binomial distribution to account for over-dispersion. To find the differentially expressed genes with a binary phenotypic response, we aim to develop a statistical test for comparing the means of two Negative-Binomial distributions. A Wald test statistic based on the pseudo maximum likelihood estimators is proposed. A numerical study is performed for justification of the proposed test. The applicability of the proposed method is demonstrated via the data analysis of two real example data sets