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Fig. 4 | BMC Genomics

Fig. 4

From: Comparison of normalization methods for the analysis of metagenomic gene abundance data

Fig. 4

Quantile-quantile plots for p-values of non-DAGs. Data quantiles for the Human gut I dataset (y-axis) were plotted against the theoretical quantiles of the uniform distribution (x-axis) for nine normalization methods. The results were based on resampled data consisting of two groups with 10 samples in each, an average fold-change of 3, for balanced (‘B’) case where 10% effects were equally distributed in the two groups and heavily-unbalanced (‘HU’) case where 20% effects were added in only one group. Each dashed line is one of the 100 iterations. Lines deviating from the diagonal indicates biased p-values. 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)

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