Respected Madam/Sir, I would like to know about contrasts matrixx between wild and mutant type with replicates. Below you can see two contrasts matrix and both have different results in term of + & - value like *7.122005 & **-7.122005 *respectivily. * c<-makeContrasts(group2-group1,levels=design) ** * topTable(fit2, coef=1, adjust="fdr", number=10) ID logFC AveExpr t P.Value adj.P.Val B 8516 253416_at *7.122005* 7.535481 26.57534 2.255100e-05 0.3000238 1.4319777 21394 266294_at *5.221736* 7.090044 24.38216 3.100325e-05 0.3000238 1.3731773 *OR **c<-makeContrasts(group1-group2,levels=design) *topTable(fit3, coef=1, adjust="fdr", number=10) ID logFC AveExpr t P.Value adj.P.Val B 8516 253416_at *-7.122005* 7.535481 -26.57534 2.255100e-05 0.3000238 1.4319777 21394 266294_at* -5.221736* 7.090044 -24.38216 3.100325e-05 0.3000238 1.3731773 Could you telll me which one is correct ? because on the basis of these value i select up/down expression ? Thanks Varpall [[alternative HTML version deleted]]