MA plots of microarray 5812 in the LYMPHOMA data set. The plots show the results before and after location normalization designed to remove intensity effect. The MA plot is a scatter plot of log ratio M = log2(R
) (abscissa) versus average log intensity (ordinate). Columns depict non-normalized (N ONRM), and normalized M
values (IG LOESS, IL LOESS, IST SPLINE, Q SPLINEG, QS PLINER, IG SG LOESS). Plots in the same row represent same data except that each plot in the left panel shows one lowess curve for all the spots (marrayPlots/maPlot(data, z = NULL)); while that in the right panel shows one lowess curve per PT group (marrayPlots/maPlot(x="maA", y="maM", z="maPrintTip")). Different colors and line types are used to represent different groups from different rows ("ngr", Figure 1) and columns ("ngc") respectively.