HI all, just a quick question about cuffdiff: when I write the imputs files, for example sample1 (untreated) and sample2(treated), does it make any difference the order? E.g., the order in which i insert the relative tophat samples? I compared 3 samples (a, b, c) each of then against a non trated sample (x), but i realised that in cuffdiff i gave in one case first the tophat of sample a and than sample x than when i ran a new cuffdiff i gave first sample x and then sample b or c....is the test statistic goign to be different?The log2fold change has the same number, just + or - depending on the order thanks, ib