I'm using cuffdiff 2.1.1 to look for differential gene expression between two conditions. Each condition has 2 biological replicates. The results I get look promising from a log fold change perspective - lots of genes that I would expect to be affected have the highest fold change values. However, from a q-value perspective very few of the results look promising, having q values > 0.05.
My question is, given 2 replicates, how is the q value calculated? Surely if there was high variance between replicates but the difference between experimental conditions was also large then the q-values would be correspondingly high?
In this case, can I, or should I, really trust the q-values?