BMC Genomics 2006, 7:252 http://www.biomedcentral.com/1471-2164/7/252 FDiigsturribeu3tion of 3' distances from probesets with the most discrepant signal intensity following TwoRA (absolute Δlog2IN >= 2) Dist ribution of 3' distances from probesets with the most discrepant signal intensity following TwoRA (abso- lute Δlog2IN >= 2). A&B, histograms of 3' locations from the probesets at large represented on the MOE430A chip (green) versus those showing at least 2 fold change in log2 signal intensity following TwoRA (increase/decrease in signal, red/blue respectively). (Solid line), DRG. (Dashed lines), SA. (Dotted lines), SN. Arrows indicate additional peaks in the distributions apart from that of the overall population. C, a box and whisker plot showing the 0% and 100% quantiles as whiskers, the 25% and 75% quantiles as boxes and the 50% quantile as horizontal dash within the box. The plot summarises the distributions shown in A and B. One the y-axis, (+) indicates increase in signal intensity following TwoRA, (-) indicates decrease in signal intensity following TwoRA. Note that for all plots, probesets locations are in base pairs and relative to the 3' end of targets. ure 3c). These results show for the first time that the most severe signal distortions following TwoRA are strongly associated with 3' positional bias. Interestingly, with both populations of deviant probesets (Figure 3a &3b), there is a peak that overlaps with that from the distribution of the average population. This Page 5 of 14 (page number not for citation purposes)