Example datasets used in manual pages and vignette by carrying out HTSeq procedure for exonic mapped reads (Observed) and non-exonic mapped reads (Background) and gene length information (genelength).
We developed a novel algorithm, XBSeq, where a statistical model was established based on the assumption that observed signals are the convolution of true expression signals and sequencing noises. The mapped reads in non-exonic regions are considered as sequencing noises, which follows a Poisson distribution. Given measureable observed signal and background noise from RNA-seq data, true expression signals, assuming governed by the negative binomial distribution, can be delineated and thus the accurate detection of differential expressed genes.
XBSeqDataSet is a subclass of "DESeqDataSet", used to store the input values, intermediate calculations and results of an analysis of differential expression. Different from the original DESeqDataSet class, XBSeqDataSet has some extra slots including:
The 'counts' function extract a certian assay element from XBSeqDataSet object. The normalized assay element can be extracted by specifying 'normalized = TRUE'.
providing 
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