Figure 3

Comparisons of different filtering methods for spike-in data. Upper panel (A): ROC curves for different filtering methods. Adaptive filtering results are based on k-means method. The line representing S_50 filtering method, in the upper panel (A) is hard to notice due to the fact that it is obstructed by other lines. Lower panel (B): Change of F1 measure versus percentage of genes filtered out by different filtering methods. 50% threshold is additionally marked with vertical black line. Circles and x-signs on the plot correspond to points given by percentages following from our adaptive filtering methods (top3 and k-means respectively) and corresponding values of the F1 measure. Different colors correspond to different filtering types of filters: red color is assigned to the filtration in sample variance domain, blue - sample mean, green - sample variance in log scale, and black - no filtration. Different line styles correspond to different methods: solid line shows the results for adaptive filtering, dashed line - fixed threshold filtering. Percentages of the removed genes after AS, AV and ALV filtering are 76.4, 86.9 and 92.8, respectively, for the top3 method, and 76.4, 76.1 and 92.8, respectively, for the k-means method.