Hi, I've performed a limma analysis on paired samples that were run on Illumina HT12 arrays, with three replicates in each condition. I'm a bit troubled by the results though, as there are several probes that have very small adjusted p-values, though when looking at the paired ratio values, they vary quite a bit. Here are a few examples where the comparison is long-short, and the samples are paired by the letters A,B,C. After the adj.P.Val column, I've calculated the paired sample ratio values, these three columns are followed by the signal intensities from each sample: ProbeID TargetID logFC AveExpr P.Value adj.P.Val long-short.A long-short.B long-short.C long.A long.B long.C short.A short.B short.C 1450390 RPL17 -1.3733092649 10.2105020267 4.35314891863083e-17 4.55305891127872e-14 -1.277287712 -0.6714209686 -2.1712191142 9.5618416199 9.5085763086 9.5011242541 10.8391293319 10.1799972771 11.6723433683 1230376 ALAS2 1.4395987013 10.0069363572 4.9058551374517e-17 4.76463659313792e-14 0.356310701 2.2275874983 1.7348979044 9.1085909827 10.4991863428 12.5724297981 8.7522802817 8.2715988445 10.8375318936 3420451 RSL24D1 -1.2585240828 8.0288125742 6.26229691539969e-15 4.73046950881609e-12 -0.9845918613 -0.6335605827 -2.1574198045 7.5348228063 7.4471358372 7.2166929547 8.5194146676 8.0806964199 9.3741127592 I'd assumed that limma would have been more sensitive to this and am wondering if anyone could please explain why this may be occurring. Thanks, Ryan __ Ryan Basom Systems Analyst/Programmer Genomics Resource Fred Hutchinson Cancer Research Center [[alternative HTML version deleted]]