Hi there, I have another question regarding limma and doing a block design on paired samples. this is how I understand this design to work, maybe someone can tell me If I got it right: the function duplicateCorrelation calculates the mean correlation between your blocked samples (in the variable $consensus) which can be used as input for the correlation parameter in the lmFit function. This variabel is then used for variance estimation in the denominator in the t-statistik formula. Is the nominator of the t-Statistik paired though (meaning the mean of the differences) ? and what do I do with a really low $consenus value like 0.03 ? best regards, Mayra