Fig. 3.

True and false positive rates for increasing unbalanced effects. (a) True positive rate at a fixed false positive rate of 0.01 (y-axis) and (b) false positive rate at a fix true positive rate of 0.50 (y-axis) for different distributions of effects between groups: balanced (’B’) with 10% of effects divided equally between the two groups, lightly-unbalanced (‘LU’) with effects added 75%-25% in each group, unbalanced (’U’) with all effects added to only one group, and heavily-unbalanced (‘HU’) with 20% of effects added to only one group (x-axis). The results were based on resampled data consisting of two groups with 10 samples in each and an average fold-change of 3. Three metagenomic datasets were used Human gut I, Human gut II and Marine. The following methods are included in the figure: trimmed mean of M-values (TMM), relative log expression (RLE), cumulative sum scaling (CSS), reversed cumulative sum scaling (RCSS), quantile-quantile (Quant), upper quartile (UQ), median (Med), total count (TC) and rarefying (Rare)