Hi

I have analyzed DEG between control vs sensitive to drug X, control vs insensitive to drug X, and sensitive vs insensitive. I used limma to find related DEGs, here is my code

fit <- lmFit(data, design)
keep <- fit$Amean > median(fit$Amean)
ebayes <- eBayes(fit[keep,], robust=TRUE, trend=TRUE)
tab <- topTable(ebayes, coef=2, adjust="BH",n=100)
colnames(design)

[1] "(Intercept)"                                            "factor(sensitivity$chemosensitivity)Rx Sensitive"

Now from limma output, I found genes with negative log fold change that are express higher in the insensitive samples and genes with positive log fold changes that are express higher in the sensitive samples, but, what I want to know is down regulated genes in each phenotype