Additional file 8 of Comparison of normalization methods for the analysis of metagenomic gene abundance data

Figure S5. True false discovery rate for p-values adjusted using Benjamini-Yekutieli method at an estimated false discovery rate of 0.05 (y-axis) for different distribution of effects between groups (x-axis): 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. 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). (PDF 40 kb)