Figure 2.

Log-ratio box-plots. (a) For the raw probe-level data in [1] we computed log fold changes comparingthe control and spike-in arrays for each of the three replicates. The C and S arrays were pairedaccording to their filenames: C1-S1, C2-S2, and C3-S3. Box-plots are shown for five groups of probes:not spiked-in (gray), spiked-in at equal concentrations (purple), spiked-in with nominal fold-changes between 1 and 2, 2 and 3, and 3 and 4 (orange). (b) As (a) but after quantile normalizing the probes.