Figure 8
Effect on biological interpretation. (A) Showing the log intensity of bead-type 5900598 from six array sections each of which had the same sample hybridized to them. The summarized intensities have been calculated twice, once using the standard analysis and once with beads affected by the identified phenomena removed. (B) & (C) show the log intensties of the individual beads of type 5900598 on section 4343238080_D_2 calculated using the standard and two-step summarization methods respectively. Histograms of the log intensities of the negative control beads calculated in the same fashion are shown down the sides. In panel (C) beads excluded due to their proximity to the phenomena identified in this study are indicated by the red cross. The dotted lines indicate the range of values outside of which beads are classed as outliers and are excluded from the summarization step. The removal of the marked bead results in three additional beads being classed as outliers. The result is a lower summarized intensity (the solid black line), which when compared to the negative control beads, changes from being classed as expressed to not expressed.