Additional file 3 of Comparison of normalization methods for the analysis of metagenomic gene abundance data

Figure S3. Mean Spearman correlation between raw and normalized counts. Spearman correlations were compute per gene before and after normalization 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 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 8 kb)