Figure 3

SNN removes sequence-dependent biases using the control experiment. Scatter plot with the GC content of the probes on the x-axis and the log-ratio between spike-in and control hybridization; shades of blue indicate the density of points, the darker the more points. The line indicates a linear fit between the GC content and the log-ratio. (a) The ratio between the spike-in and control intensities on a logarithmic scale centered on the respective mean log intensities. The GC content and the log-ratio correlate with a Pearson correlation coefficient r = 0.26. (b) The same ratio after division by the standard deviation. Here, the GC content and the log-ratio are not correlated anymore (r = -0.02).