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Figure 2 | BMC Bioinformatics

Figure 2

From: Spatial normalization improves the quality of genotype calling for Affymetrix SNP 6.0 arrays

Figure 2

Image plots of glog transformed intensities against their locations on the array. The plots correspond to the first array in Set 1 (see Method Section). Colors are proportional to percentiles of the signals; white pixels correspond to non-replicated probes. (a) Raw data: no regional trend is apparent. Median (IQR) = 1150 (562, 2035). (b) Median-centered data: patterns of spatial biases become visible across the array. Median (IQR) = 0.0000 (-0.0360, 0.0362). (c) Wavelet denoising strengthens the evidence for various sources of spatial imperfection. Median (IQR) = -0.0019 (-0.0315, 0.0285). Note: wavelet surface was independently estimated from 4 regions separated by the white bands.

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