Hello Bioconductor users, We have carried the following experiment: two different fly strains (58 and 104) were tested (each) under two different conditions, Control and Pulse (C and P). For each strain, samples from two conditions were labelled with Cy3 and Cy5 and hybridized together to the same array. Two (biological) replicates were carried for each hybridization. We are interested in finding those genes for which the difference C-P is maximized (and significant) between the strains. In other words, we are interested in the difference of the differences: (C[58]-P[58]) – (C[104]-P[104]). The target file looks like that: SlideNumber FileName Cy3 Cy5 1 58 UP1_LP1.gpr control pulse 2 58 UP2_LP2.gpr control pulse 3 104 UP1_LP1.gpr control pulse 4 104 UP1_LP1.gpr control pulse Could anyone please help us with writing the design and contrast matrix for analysing this experiment with Limma? Many thanks, Eran Eran Tauber (PhD) Lecturer in Molecular Evolution Dept. of Genetics University of Leicester University Rd, Leicester LE1 7RH England ____________________________________________________________ Phone: 44 (0)116 252-3455, 252-3421 (lab) Fax: 44 (0)116 252-3378 www.le.ac.uk/genetics/et22 [[alternative(swapped) HTML version deleted]] This is MIME Epilogue