ts

ase two logarithm fold change (log2FoldChange) and the

p value (padj) can be used to draw a volcano plot. Figure 6.11

e six-panel volcano plot for the airway data, where 62 down-

DEGs and 89 up-regulated DEGs were displayed.

The six-panel volcano plot for a DESeq model constructed for the airway data.

cover DEGs for sequencing count data using edgeR

onductor package edgeR [Robinson, et al., 2009] can also be

iscover DEGs based on the sequencing count data. The airway

used again to show how edgeR works. The following function

d to generate a working data, where counts was a sequencing

trix, groups defined sample class labels (experimental design)

es was a gene symbol vector,

Z0=DGEList(counts,group,genes)

working data Z0 was a list. It was composed of three entries,

was a count matrix, samples was a matrix of samples as well

normalisation factors (being one) and genes was a vector of

bols. Based on the working data Z0, the counts were normalised

e following function, which aligned the counts based on the

ation factors calculated from the count matrix.