Figure 3.17: Ratio of expression level as a function of position. The ratio of the two different dye intensities per gene for a single microarray plotted against the position in the array (defined as a single number that is computed from the x and y coordinates of the probe on the array). The "control islands" that contain "spiked" controls on the array were not included in this plot. Also, all expression values were corrected for background noise. No particular pattern is obvious on inspection. An eyeball inspection across thousands of data points as we have done above with the Incyte expression data set is often not sufficient for detecting subtler and less visually prominent patterns in the data representation. By applying standard signal-processing techniques such as the discrete Fourier transform, we find several major frequency peaks in the expression level across the chip (see figure 3.18). The highest peak here occurs at a frequency of 4 per array surface. This kind of periodic pattern in the Fourier transform expression data appears to be location dependent, and should lead the analyst to suspect that something systematically amiss occurred during the generation of this data set which could have happened during the manufacturing, hybridization, or the scanning stages.

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