Table 4.

Simulation studies (two batch groups): summary of accuracy measurements before and after batch effect correction. The proportion of correctly identified microbial variables with a true treatment effect was assessed with Precision, Recall, F1 score (using one-way ANOVA as variable selection procedure) and AUC (using sPLSDA as variable selection procedure). Each value is the mean (or standard deviation) over 50 repeats.

		Before correction	ground-truth data	SVA	removeBatchEffect	ComBat	PLSDA-batch	sPLSDA-batch
Balanced	Precision	0.984 (0.04)	0.952 (0.08)	0.957 (0.06)	0.950 (0.09)	0.952 (0.08)	0.952 (0.08)	0.807 (0.11)
	Recall	0.674 (0.03)	0.900 (0.03)	0.934 (0.03)	0.910 (0.03)	0.911 (0.03)	0.910 (0.03)	0.910 (0.03)
	F1	0.799 (0.02)	0.923 (0.05)	0.944 (0.04)	0.927 (0.05)	0.929 (0.05)	0.929 (0.05)	0.851 (0.06)
	AUC	0.944 (0.02)	0.964 (0.02)	/	0.968 (0.02)	0.968 (0.02)	0.969 (0.01)	0.954 (0.02)
		Before correction	ground-truth data	SVA	removeBatchEffect	ComBat	wPLSDA-batch	swPLSDA-batch
Unbalanced	Precision	0.385 (0.01)	0.973 (0.05)	0.401 (0.02)	0.901 (0.09)	0.834 (0.08)	0.943 (0.05)	0.943 (0.05)
	Recall	0.825 (0.03)	0.895 (0.03)	0.918 (0.03)	0.910 (0.03)	0.919 (0.03)	0.888 (0.03)	0.862 (0.03)
	F1	0.525 (0.01)	0.932 (0.03)	0.558 (0.02)	0.903 (0.05)	0.873 (0.05)	0.914 (0.03)	0.900 (0.03)
	AUC	0.704 (0.06)	0.967 (0.02)	/	0.963 (0.02)	0.962 (0.01)	0.965 (0.01)	0.954 (0.02)