FIG. 2.

Representative MA plots from the amino acid data set. (A to I) MA plots, each comparing two different microarray datasets (array¹ versus array²) from this analysis. M is plotted on the y axis and is given by log₂[array¹ intensity/array² intensity]. Therefore, M equals 0 when the intensities across two arrays are equal. A is plotted on the x axis and is given by 0.5(log₂[array¹ intensity] + log₂[array² intensity]). This is the average of the intensities across the two arrays. For the biological replicates (e.g., PC1 versus PC2, MC1 versus MC2, MS1 versus MS2, PS1 versus PS2, or TC1 versus TC2), the M values cluster tightly around 0, whereas for the control-versus-stress comparisons (e.g., PC1 versus PS1, MC1 versus MS1, or TC1 versus TS1) or for the polysome-versus-monosome sample comparisons (e.g., MS1 versus PS1), the M value is more dispersed. The σ² value for each data set is depicted in the top left corner of the plots and gives a standard statistical measure of the variance in M.