Fig. 3

Reliability of identifying differentially expressed features. a Schematic diagram of comparisons of differentially expressed features (DEFs) between cross-batch and intra-batch datasets with reference datasets. b-c Bar plots (mean ± s.e.) representing the relative correlation (RC) (b) and Matthews Correlation Coefficient (MCC) of DEFs (c) with reference datasets and across seven BECAs in balanced and confounded scenarios using transcriptomics, proteomics, and metabolomics data. Mean value of the dataset without correction (raw) in each panel was plotted in dashed line. Performances between the raw group and BECA groups were compared using Student’s t-test. A group with the performance significantly higher than raw group was marked with stars (*). Symbolic number coding of p-value was used as: *** (p ≤ 0.001), ** (0.001 < p ≤ 0.01), * (0.01 < p ≤ 0.05)