RNA-seq analysis - q-values in cuffdiff
q-value is the corrected p-value to account for multiple testing (i.e. you are testing thousands of genes). Those with q-value &lt;0.05 are significant experiment-wise. Cuffdiff uses Benjamini-Hochberg correction to compute FDR (i.e. q-value). The calculation does not depend on the number of replicates it's based on the distribution of p-values those, yes, are influenced by the number of replicates. The more replicates you have the better).