3 Differential expression analysis
3.1 Analysis method
An important feature LivestockExp offers is the capability to select samples from different experimental conditions (tissues, developmental stages, stress treatments) and compare their gene expression and alternative splicing profiles. Two commonly used differential expression methods, DESeq2 and edgeR, were used to compare overall gene expression while statistical models implemented in rMATS were used to compare alternative splicing.
When possible (study not completely confounded with treatment), batch effects due to studies were adjusted using DESeq2 or edgeR. The next step is enrichment analysis based on differently expressed genes and differently spliced genes.