Correlation between position and intensity of probes. Correlation between position and intensity of probes for present probe sets in one-cycle and two-cycle amplification microarray data. X-axis is the distance of probe (the 13th nucleotide) from 3’end of its corresponding transcript, while Y-axis is the mean PM intensity of probes at each position. Microarray data generating using one-cycle (red), two-cycle (green) RNA labeling protocols are plotted respectively. We only plot the probes within 600bp of 3’ end on transcripts (account for 98.68% of the present probesets). It’s obvious that variation in two cycle is larger and the bias is more serious.