. 2025 Feb 25;16:1484183. doi: 10.3389/fmicb.2025.1484183

Table 3.

PERMANOVA R² of HIVRC dataset.

Method	Distance metric
	Bray-curtis	Aitchison	Canberra	Manhattan
Original	0.1199^*	0.0642^*	0.0808^*	0.0879^*
MMUPHin	0.0822^*	0.0602^*	0.0779 ^*	0.0295^*
Percentile normalization	0.1191^*	0.0899^*	0.1142^*	0.1136^*
ConQuR	0.0149^*	0.0901^*	0.1628^*	0.0087^*
ComBat	0.0637^*	0.0564 ^*	0.0825^*	0.0137^*
Proposed model	0.0128 ^*	0.0854^*	0.1493^*	0.0065 ^*

PERMANOVA R² represents the proportion of total variance explained by differences between groups (Anderson, 2014; Kelly et al., 2015). In this study, it was utilized to assess whether differences between groups were reduced by comparing the data before and after batch effect correction. A lower R² value indicates that the batch effect correction was successfully performed. The values in bold represent the cases where batch correction was most effectively performed for each distance metric. Significant values (P ≤ 0.05) are denoted by an asterisk (^*).