Figure 1.

Ratio-intensity plots for three methods of data processing. Horizontal axes represent the average log₂(red) and log₂(green) signal as a measure of spot intensity. The vertical axes represent the log-ratio of red and green signal. These ratio-intensity plots are for replicate 1 from Site 1, RNA A (AGL_1_A1 in the nomenclature of [6]). Blue points are ERCs with true log-ratio = ± log₂(10) ≈ ± 3.32; green points are ERCs with true log-ratio = ± log₂(3) ≈ ± 1.59; red and yellow points are ERCs with true log-ratio = log₂(1) = 0; black points are non-ERCs and have true log-ratio = 0. Top panel: noBA data (loess normalization, no background adjustment). Middle panel: BA data (loess normalization, with background adjustment). Bottom panel: FE data (data processing by Feature Extraction).