Fig. 3.

Fragment-size effect in pre- and post-normalized data from a normal mouse spermatogenic sample. The data is divided into 58 step-wise bins each containing a comparable number of HTFs. The color key at the upper left illustrates the partitioning scheme for pre-normalized data where each colored block corresponds to a bin of certain HTF sizes; color varies from blue to red with increasing fragment size (from 200–2,000 bp). The density of MspI signal intensities for each bin is shown in panel (A), where different color lines represent the density data for HTFs from each corresponding bin. The black line represents the overall density of MspI intensity data. Panel (B) shows the same representation for HpaII signals and panel (C) shows the same representation for HpaII/MspI ratios. The color key to the lower left shows the analogous partitioning scheme for normalized data after failed probes have been identified and removed. Normalized MspI, HpaII, and HpaII/MspI ratio data are shown (without failed probes) in panels (D), (E), and (F), respectively.