Next – Generation Sequencing

DESeq2 will normalize the counts and parameters based on the number of samples, dispersion,
variation between replicates, etc. Once the analysis is complete save the results in new variable
“res”.

res=results(dds)

Visualize DE results by creating MA (Fig. 5) and Volcano plots

plotMA(res, main=“DESeq2”, ylim=c(-10,10), alpha=0.1)

For generating volcano plot (Fig. 6) install and load Bioconductor package “a4Base”

require(BiocInstaller)
biocLite(“a4Base”)
require(a4Base)
volcanoplotter(logRatio = res$log2FoldChange, pValue = res $pvalue, pointLabels =
rownames(res), topPValues = 3, topLogRatios = 3)