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Figure 2 | BMC Bioinformatics

Figure 2

From: Quality assessment of microarrays: Visualization of spatial artifacts and quantitation of regional biases

Figure 2

Regional biases on an Affymetrix chip. An Affymetrix chip is represented in log2 scale at upper left and the ratio of the same Affy chip to the standard chip at upper right. Each pixel of the original image represents one probe. The color legend is shown at bottom; bright red represents off-scale high, and white represents off-scale low. Blue rectangles in the upper plots indicate non-coding probes. In the lower row are images for background and scale factor for the same chip. The left plot represents the local background – the lowest levels achieved by probes on this chip relative to the lowest levels achieved by probes in the same region in other chips. The lower right plot represents the effective sensitivity or local scale factor – the log ratio of values of typically bright probes on this chip, to their values across the other chips. The scale factor captures all the variation seen in the top right image while the background image shows almost no variation. This clear separation between background artifacts and scale factor artifacts is typical in Affy chips. This chip is within the range of acceptable by our QC protocol (see discussion).

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