dear @Yasyou,
it depends what you define by paired data!
Same samples measured across 2 omics: yes
Samples measured twice (i.e. before/after): you would need to account for the repeated measurements using a multilevel approach. There has been quite some discussions already on that topic if you search, for example: sPLS-DA model for repeated longitudinal measurements - #2 by kimanh.lecao
Cheers,
Kim-Anh