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Figure 2 | BMC Bioinformatics

Figure 2

From: Empirical array quality weights in the analysis of microarray data

Figure 2

Number of false discoveries from simulated data sets with 3 arrays. For each 3 array simulation in Table 2 (1, 2 and 3), the average false discovery rates calculated using ordinary t-statistics (solid lines) or moderated t-statistics (dashed lines) are given. Panels (a), (c) and (e) show the results for normal data under simulations 1, 2 and 3 respectively while panels (b), (d) and (f) display the corresponding results for non-normal data. Black lines plot the false discovery rates when the most unreliable array is removed from the analysis. Light gray lines are the results obtained using equal weights and dark gray lines show the false discovery rates recovered with array weights. Each line is the average of 1000 simulated data sets. In nearly all cases, the use of array weights in the analysis gives fewer false positives than the other methods. Simulation 1 is the exception, with equal weighting and array weighting producing similar false discovery rates (overlapping curves) for both normal (a) and non-normal (b) data.

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