Additional data file 3.
A. Histograms of log2 MFI values obtained from wells containing sample material (white) and blank control wells (blue). B. The number of detected probes after filtering was plotted against a range of cutoff values. Probes were removed (filtered) if they did not exceed the chosen cutoff (red) in at least one sample. C, D. Sample quality control. Pearson correlation coefficients for technical replicate samples were plotted against the smaller of the two sample means for (C) cell line technical replicate samples and (D) normal and tumor technical replicate samples. The cutoff used for quality control is indicated by a vertical line. Colours corresponding to sample status are explained in the colour key. E. Technical sample effects. Pairwise differences between the medians of technical replicate samples were plotted for unnormalized data (black), data normalized based on spike-in controls (blue) and data normalized by sample median centering (red). Dashed lines indicate the maximum difference between the medians of any two samples for unnormalized data (black) and for data normalized using spike-in controls (blue).
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Blenkiron et al. Genome Biology 2007 8:R214 doi:10.1186/gb-2007-8-10-r214