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The disparity in the amount of probe printed is a major source of pin difference in microarrays. Using one hybridization from the rat thymus experiment, we calculated the mean (A) and the SD (B) in log ratio for data under each pin, and plotted them against the percentage of spots with TD intensity below 5,000 RFU/pixel. There is a clear increase of SD when there are more poor-quality spots under the corresponding pin.
