Hi,

I'm using Limma for DE of microarray data. But logFC values in the topTable are not correct, and actually I got the minus values of the two conditions C1 and C2: mean(C1)-mean(C2).

>head(dat_mean)

                    mock_EGF_mean1 mock_EGF_mean2 mock_no_mean1 mock_no_mean2
p63(Phospho-Ser455)          10720          12198          8806          6693
p53(Phospho-Thr81)           24904          26344         24109         23845
p53(Phospho-Thr18)           24353          25907         10325         13047

                    WT_EGF_mean1 WT_EGF_mean2 WT_no_mean1 WT_no_mean2
p63(Phospho-Ser455)        11679        11527        4240        4485
p53(Phospho-Thr81)         23098        24763       22169       25038
p53(Phospho-Thr18)         19030        22638       14085       13643

>design <- cbind(mock.EGF=c(1,1,0,0,0,0,0,0),mock.no=c(0,0,1,1,0,0,0,0),
                WT.EGF=c(0,0,0,0,1,1,0,0),WT.no=c(0,0,0,0,0,0,1,1))

>fit <- lmFit(dat_mean, design)
>cont.matrix <- makeContrasts(mock_LigvsNo=mock.EGF-mock.no,WT_LigvsNo=WT.EGF-WT.no,Lig_MockvsWT=mock.EGF-WT.EGF, No_MockvsWT=mock.no-WT.no,levels=design)
>fit2 <- contrasts.fit(fit, cont.matrix)
>fit2 <- eBayes(fit2)

>results <- decideTests(fit2)

>AA1<-topTable(fit2,coef=1,number=30,adjust="BH")
>AA2 <- topTable(fit2,coef=2,number=30,adjust="BH")
>AA3 <- topTable(fit2,coef=3,number=30,adjust="BH")
>AA4 <- topTable(fit2,coef=4,number=30,adjust="BH")

Any comments/suggestions are highly acknowledged!

Dawn