Table 3 Results of seven regression models. For each model (outcome measure) we indicate if (i) outliers and/or dataset D3/D4 were removed, (ii) covariates were standardized to zero mean and unit standard deviation, and (iii) outcome measures were log-scaled. For each model the overall significance of the model (ANOVA) and the significant model coefficients are shown. The +/− indicate a positive/negative effect in relative to the model intercept (approach A3). Note that the pairwise comparison for A5-A9 is just above our threshold of 0.05. The four pairwise comparisons shown in bold correspond to the pre-defined comparisons shown in Fig. 2. The asterisk denotes comparisons between CF reconstruction methods (A3-A10). Padj is the Holm–Bonferroni adjusted p-value. A = approach, SD = sequence depth; ML = mutation load
From: Systematic evaluation of B-cell clonal family inference approaches
Outcome variable | Removal outliers and/or D3/D4 | Covariate standar- dization | Log10 scaling | Overall significance (ANOVA) | Significant model coefficients (p-value) | Significant pairwise comparisons (padj) |
|---|---|---|---|---|---|---|
Number of Clonal Families (CF) | Outliers | Yes | Yes | A (p < 0.001) SD (p < 0.001) ML (p < 0.001) | -A6 (< 0.05) -A9 (< 0.05) +SD (< 0.001) -ML (< 0.001) | A2-A6 (0.0024) A2-A9 (0.0011) A10-A6 (0.0229)* A10-A9 (0.0120)* |
Singletons | D4 | No | Yes | A (p < 0.001) SD (p < 0.001) ML (p < 0.001) | +A2 (< 0.05) -A6 (< 0.05) -A9 (< 0.001) -A10 (< 0.05) +SD (< 0.001) -ML (< 0.001) | A1-A9 (0.0104) A2-A4 (0.0414) A2-A5 (0.0191) A2-A6 (<.0001) A2-A9 (<.0001) A3-A6 (0.0371)* A3-A9 (0.0037)* A4-A9 (0.0246)* A5-A9 (0.0521)* A10-A2 (0.0002) |
Mean CF size | None | No | Yes | A (p < 0.0001) SD (p < 0.05) ML (p < 0.001) | +A6 (< 0.05) +A9 (< 0.05) -SD (< 0.05) +ML (< 0.001) | A2-A6 (0.0019) A2-A9 (0.0008) A10-A6 (0.0183)* A10-A9 (0.0094)* |
Number of Dominant Clones (0.5%) | None | Yes | Yes | ML (p < 0.001) | +ML (< 0.001) | None |
D50 | Outliers | No | Yes | A (p < 0.05) SD (p < 0.001) ML (p < 0.001) | +SD (< 0.001) -ML (< 0.001) | None |
Gini-Simpson index | Outliers D3 | Yes | Yes | A (p < 0.05) SD (p < 0.001) ML (p < 0.001) | +SD (< 0.001) -ML (< 0.01) | A2-A6 (0.0463) |
Shannon index | Outliers | No | No | SD (p < 0.001) ML (p < 0.001) | +SD (< 0.001) -ML (< 0.001) | None |