Summary of results from the FDR analysis. The median value for the number of true positives detected, the number of false positives detected and achieved true FDR at a cutoff of 0.05 estimated FDR for both data sets. The group sizes were set to 6â+â6 and the effect size to 5. The results were based on 100 resampled metagenomes. (DOCX 15 kb
Table S1. True positive rate at a fixed false positive rate of 0.01 for a group size of 10+10. (PDF ...
The p-value distributions for the Qin dataset for the remaining methods. For the quantile-quantile-p...
Figure S2. Scatterplot of normalization factors for each pair of scaling methods. Normalization fact...
Area under curve estimates on unfiltered data for all 14 methods. Higher values represent higher gen...
The full area under curve estimates at different group sizes for all 14 methods. Higher values repre...
The gene ranking performance at different effect sizes for all 14 methods. Each listed value is the ...
The full area under curve estimates at different effect sizes for all 14 methods. Higher values repr...
Ranking performance at increasing effect size for the main methods. The effect size (fold change) in...
Ranking performance at increasing group size for the remaining methods. For each method, the receive...
The abundance of zeroes averaged over resampled data sets. There is a large difference in the number...
Table S2. False positive rate at a fix true positive rate of 0.50 for a group size of 10+10. (PDF 16...
Differentially expressed genes in bodies. Table includes all genes surviving a genomewide FDR thresh...
The p-value distributions for the Yatsunenko dataset for the remaining methods. For the quantile-qua...
Figure S4. Effect size analysis of DAGs. Estimated effect size of differentially abundant genes (DAG...
Figure S1. Histograms of Spearman correlations between normalization factors and raw counts of non-d...
Table S1. True positive rate at a fixed false positive rate of 0.01 for a group size of 10+10. (PDF ...
The p-value distributions for the Qin dataset for the remaining methods. For the quantile-quantile-p...
Figure S2. Scatterplot of normalization factors for each pair of scaling methods. Normalization fact...
Area under curve estimates on unfiltered data for all 14 methods. Higher values represent higher gen...
The full area under curve estimates at different group sizes for all 14 methods. Higher values repre...
The gene ranking performance at different effect sizes for all 14 methods. Each listed value is the ...
The full area under curve estimates at different effect sizes for all 14 methods. Higher values repr...
Ranking performance at increasing effect size for the main methods. The effect size (fold change) in...
Ranking performance at increasing group size for the remaining methods. For each method, the receive...
The abundance of zeroes averaged over resampled data sets. There is a large difference in the number...
Table S2. False positive rate at a fix true positive rate of 0.50 for a group size of 10+10. (PDF 16...
Differentially expressed genes in bodies. Table includes all genes surviving a genomewide FDR thresh...
The p-value distributions for the Yatsunenko dataset for the remaining methods. For the quantile-qua...
Figure S4. Effect size analysis of DAGs. Estimated effect size of differentially abundant genes (DAG...
Figure S1. Histograms of Spearman correlations between normalization factors and raw counts of non-d...
Table S1. True positive rate at a fixed false positive rate of 0.01 for a group size of 10+10. (PDF ...
The p-value distributions for the Qin dataset for the remaining methods. For the quantile-quantile-p...
Figure S2. Scatterplot of normalization factors for each pair of scaling methods. Normalization fact...