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