198    ◾    Bioinformatics

Figure 5.24 shows the number of downregulated, nonsignificant, and upregulated genes at

the threshold of 2 log-fold change and 0.05 significance level.

The level of the differential gene expression change can be visualized with the mean-

difference plot (MD plot):

jpeg(‘mdPlotfitted.jpg’)

my.contrasts

<- makeContrasts(conditiontumo-conditionnorm,levels=design)

fitq<-glmQLFit(yNorm, design)

qlfq<-glmQLFTest(fitq, contrast=my.contrasts)

DEGenes<-decideTestsDGE(qlfq,

adjust.method=”BH”, p.value=0.05, lfc=2)

plotMD(qlfq, status=DEGenes,

FIGURE 5.23  Differential analysis with log-fold change threshold.

FIGURE 5.24  The number of downregulated, upregulated, and nonsignificant genes.