Figure 3. Task 1—Reflection of batch characteristics.

Metric scores versus (surrogate) batch strength across the real datasets. Summarized metric scores (y-axis) are compared with the proportion of DE genes (top x-axis, solid line) and the mean PVE-Batch (bottom x-axis, dashed line) per dataset. Datasets with a stronger batch effect (high percentage of DE genes/mean PVE-Batch) are expected to show a higher overall metric score than datasets with mild batch effects (low percentage of DE genes/mean PVE-Batch). Spearman correlation coefficients of metrics against the two batch strength measures are shown (R_PVE-Batch, R_DE) in the text boxes for each metric and evaluated in Task 1. Metric scores were standardized by subtraction of their minimum and division of their range (maximum–minimum) across datasets. Directions were adjusted when necessary, such that all scores increase with batch strength.