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A smaller average coefficient of variation between replicates was obtained with the latter approach, and therefore we opted to use only the Cy5-labeled sample measurements to calculate the treatment:control sample ratios.

High correlations between sequencing replicates were obtained (Pearson's correlation coefficients and R values greater than 0.98 and 0.95, respectively; Additional files 7, 8 and 9), and read counts were summed to obtain better coverage and improve variance estimation of each biological replicate [ 47].

All replicates were obtained from independent experiments.

Three biological replicates were obtained under each condition described above.

Three array replicates were obtained for each condition.

Three technical replicates were obtained for each RNA pool.

Two spectra from three biological replicates were obtained.

Two technical replicates were obtained for each microarray experiment.

For each condition, three biological replicates were obtained.

Especially with NM, the variation between replicates was large and even negative accuracies were obtained, although in a very small proportion of the replicates (5.5% of replicates).

Again, a high correlation factor (above 0.99) was obtained between replicates (data not shown).