sSeq: A Simple and Shrinkage Approach of Differential Expression Analysis for RNA-Seq experiments

In this section, we will use the Hammer et. al. data [1] to illustrate how to use the functions in the sSeq package. The two conditions are control Sprague Dawley after 2 months (Condition A) and L5 SNL Sprague Dawley after 2 months (Condition B). There are two samples within each condition. This data is included in the sSeq package as an example, and can be imported as follows. “countsTable” is a matrix or data frame in which a column represents a sample and a row represents a gene. “conds.Hammer” is a characteristic vector, and used to define the conditions corresponding to the samples in columns. After defining the input counts table and the groups for conditions, the function “nbTestSH” can be utilized to obtain the regularized dispersion estimates and perform the exact tests. The output is a data frame in which the “pval” column includes the p-values of the exact tests.