Hello,
I am using limma to analyse my gene expression data. I have the expression data from the wild-type (WT) and mutant (M) strains, in two conditions: stimulated (S) and unstimulated (U). This is how my contrast matrix looks like:

cont.matrix <- makeContrasts(
WT=WT.S-WT.U,
M=M.S-M.U,
WTM=M.U-WT.U,
levels=design)

I just want to make sure:
If we consider the contrast WT=WT.S-WT.U, a positive value of logFC would be interpreted as an up-regulation in the stimulated condition?

Thanks for help.

Yes, assuming you've set it up as a one-way layout or something similar where each coefficient in design represents the average log-expression of the group after which it is named.