Hello,

I used Limma in R in order to find differentially expressed genes from 10 samples compared to reference(control)

contrast.matrix <- makeContrasts(RF_control= RF-control, LNIT_control= LNIT-control, REC_control= REC-control, LIP_control=LIP-control, BUR_control= BUR-control,BRI_control=BRI-control, UL_control=UL-control, FF_control=FF-control, LT_control=LT-control, LTMAS_control= LTMAS-control, levels=design )

I set to just return twofold up or down regulated genes (nrow(topTable(eFit, coef=1, number=10000, lfc=2)))

at the end I just get on file as results with logFC AveExpr, t, p.value,....

Unfortunaltly this file is not really much help, did i define the matrix in a wrong way?