Additional file 2 of Comparison of normalization methods for the analysis of metagenomic gene abundance data

Figure S2. Scatterplot of normalization factors for each pair of scaling methods. Normalization factors estimated per sample in the Human gut I, for group size 10+10, with 10% of effects divided equally between the two group, and fold-change 3. Affected genes were randomly selected in 100 iterations. The number on the top-left of each plot indicates the Spearman correlation for the normalization factors presented in the plot. 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), upper quartile (UQ), median (Med) and total count (TC). (PDF 316 kb)