BMC Genomics 2006, 7:252 http://www.biomedcentral.com/1471-2164/7/252 DFiegvuiarteio2n in log2 intensity following TwoRA (Δlog2IN) as a function of probeset 3' distance rank Deviation in log2 intensity following TwoRA (Δlog2IN) as a function of probeset 3' distance rank. Δlog2IN values on the y-axis were calculated by subtracting the mean OneRA from the mean TwoRA probeset log2 intensities. The x-axis shows the ranks of probesets locations. Probesets locations are relative to the 3' end of the transcripts (refer to methods for more details). Since the probesets locations have a skewed distribution, their ranks were plotted instead of their absolute val- ues; this allows dispersion of data points. The actual probesets locations that correspond to the rank intervals on the x-axis are shown on the blue horizontal axis on the top of the figure. The regression line is shown in red. Only data from the DRG prep- aration were used, similar results were obtained with the SN and In a separate but related analysis, probesets whose abso- lute Δlog2IN values were greater than 2 were reviewed for their 3' location distribution (Figure 3). This was com- pared to the distribution of 3'location of all probesets on the array. The distribution for all probesets appears to be skewed and peaks at around 600 bp. The distribution of probesets with intensified signal shows an additional peak to the left suggesting a distinct population of probesets closer than average to the 3' end (Figure 3a). This is further highlighted by a decrease in the 25% quan- tile relative to the overall population in the boxplots on figure 3c. Conversely, the distribution from probesets with attenuated signal shows a second peak to the right indicating an overrepresentation of more distal interroga- tion points relative to the 3' end of targets (Figure 3b). This corresponds to an increase in the 75% quantile (Fig- Page 4 of 14 (page number not for citation purposes)