Figure 3.

Post-normalization MA plots. MA plots show log fold changes (M) as a function of the mean single channel intensity (A). Columns show the effect of pre-processing methods. The two arrays shown in the rows are typical of results seen with Agilent chips. The Agilent normalized MA plot exhibits large variablity at low intensities and a low intensity bias toward positive fold changes. Background subtracted, loess normalized MA plots of median or mean fold changes are more variable than the same MA plots when background is not subtracted.